Challenges to State and Local Vaccine Mandates in New York

By Mary Beth Morrissey, Thomas G. Merrill and Christopher C. Palermo

December 10, 2021

Challenges to State and Local Vaccine Mandates in New York


By Mary Beth Morrissey, Thomas G. Merrill and Christopher C. Palermo

In various places throughout the country, and here in New York, state and local governments have adopted COVID-19 vaccine mandates in hopes of bringing an end to the pandemic, which, as of December 9, 2021, has killed more than 790,000 people in the United States.[1] The federal government has also attempted to jump into the fray, but its mandates have thus far failed to withstand legal challenges. The United States Occupational Safety and Health Administration (“OSHA”) issued a vaccination mandate under an Emergency Temporary Standard, which has been stayed by the United States Court of Appeals for the Fifth Circuit.[2] OSHA has now suspended implementation and enforcement of its mandate.[3]  Similarly, a federal mandate applicable to entities covered by the Centers for Medicare and Medicaid Services (“CMS”)[4] has been preliminarily enjoined by two federal district courts,[5] one of which issued a nationwide injunction, finding that “the government defendants do not have the authority to implement the mandate.”[6] The U.S. Department of Health and Human Services has appealed both decisions, but has suspended implementation and enforcement of the CMS mandate as well.[7]

Many legal organizations have weighed in with their positions on a vaccine mandate, including the New York State Bar Association, whose Executive Committee approved a resolution in August 2021 recommending that health care workers be vaccinated. Federal, state, and local mandates have predictably prompted lawsuits pitting individuals and organizations asserting constitutional liberties against governmental authorities seeking to act to protect the public’s health. Various state governments and others have also challenged federal mandates.

The elimination of a religious exemption to New York State’s mandates has been the focus of several lawsuits. Two cases brought in federal court alleged First and Fourteenth Amendment violations because New York’s emergency rule mandating vaccination for certain state workers does not allow a religious exemption. One federal district court, in the Northern District of New York, granted injunctive relief, enjoining the emergency rule to the extent it prevented healthcare workers from being eligible for an exemption based on their religious beliefs, concluding that the State’s emergency rule was not neutral and conflicted with healthcare workers’ federally protected right to seek a religious accommodation.[8]  The other district court, in the Eastern District of New York, denied injunctive relief without issuing an opinion.[9]

On November 4, 2021, the U.S. Court of Appeals for the Second Circuit considered the appeals in the two district court cases together, issuing a lengthy opinion holding that the plaintiffs in both cases failed to establish a likelihood of success on their claims.  The Second Circuit affirmed the denial of the preliminary injunction by the district court in the Eastern District of New York and reversed the preliminary injunction entered by the district court in the Northern District of New York.[10]   On plaintiffs’ Free Exercise claim, the Second Circuit concluded that plaintiffs had not met their burden to show that the challenged vaccine mandate is not a neutral law of general applicability under Employment Division, Department of Human Resources of Oregon v. Smith[11]  or that the mandate does not satisfy rational basis review.[12] The Second Circuit concluded that, “[f]aced with an especially contagious variant of the virus in the midst of a pandemic that has now claimed the lives of over 750,000 in the United States and some 55,000 in New York,” the State’s vaccine mandate was “a reasonable exercise of the State’s power to protect the public health.”[13]    Nor did the plaintiffs demonstrate to the Second Circuit that it was impossible for employers to comply with both the state mandate and Title VII of the Civil Rights Act of 1964, as plaintiffs would be required to show to succeed on a preemption claim.[14] The Second Circuit also rejected plaintiffs’ assertion that they were likely to succeed in establishing that the vaccine mandate violates their fundamental Fourteenth Amendment rights to privacy, medical freedom, or bodily autonomy.[15]

On November 12, 2021, the Second Circuit unexpectedly issued a per curiam “clarifying opinion” in connection with the same appeal, addressing whether employers may grant religious accommodations that allow employees to continue working while unvaccinated at positions in which, if they were infected with COVID-19, they could potentially expose other personnel, patients or residents to the disease.[16]  Key language in that opinion states:

Of course, Title VII does not obligate an employer to grant an accommodation that would cause “undue hardship on the conduct of the employer’s business.” See 42 U.S.C. § 2000e(j). And, as we also observed in our opinion, Contrary to the Dr. A.  Plaintiffs’ interpretation of the statute, Title VII does not require covered entities to provide the accommodation that Plaintiffs prefer—in this case, a blanket religious exemption allowing them to continue working at their current positions unvaccinated.” 2021 WL 5121983, at *17. To repeat: if a medically eligible employee’s work assignments mean that she qualifies as “personnel,” she is covered by the Rule and her employer must “continuously require” that she is vaccinated against COVID-19. 10 N.Y.C.R.R.  § 2.61. As we observed, this requirement runs closely parallel to the longstanding New York State requirements, subject to no religious exemption, that medically eligible healthcare employees be vaccinated against rubella and measles. 2021 WL 5121983, at *13.

The preliminary injunction entered by the district court in Dr. A. v. Hochul on October 12, 2021, has been vacated. See We The Patriots USA, Inc. v. Hochul, No. 21-2179,  and Dr. A. v. Hochul, No. 21-2566, 2021 WL 5103443, at *1 (2d Cir. Oct. 29, 2021). New York State’s emergency rule requiring that healthcare facilities “continuously require” that certain medically eligible employees—those covered by the Rule’s definition of “personnel”—are vaccinated against COVID-19, is currently in effect. 10 N.Y.C.R.R.  § 2.61.[17]

Days before the Second Circuit’s opinions, the U.S. Supreme Court, without opinion, refused to enjoin Maine’s vaccine mandate for health care workers notwithstanding their religious objections.[18] Justice Gorsuch issued a strong dissent, however, joined by Justices Thomas and Alito, stating that Maine’s refusal to provide a religious exemption “doesn’t just fail the least restrictive means test, it borders on the irrational.”[19]

Local mandates have also been issued and challenged.  The New York City Department of Health and Mental Hygiene issued an order prohibiting anyone from working in or visiting a New York City school without providing proof that they have received at least one dose of COVID-19 vaccination. The order, which was revised twice since it was originally issued in August and most recently was approved by the city’s board of health on September 17, 2021, currently provides no opportunity to undergo weekly testing in lieu of vaccination, and states that it should not be construed “to prohibit any reasonable accommodations otherwise required by law.”[20]

A group of New York City Department of Education employees challenged the city’s Department of Education vaccine mandate in Maniscalco v. New York City Dep’t of Educ., asserting that it violated their substantive due process and equal protection rights under the 14th Amendment, and was arbitrary and capricious. The district court denied plaintiffs’ motion for a preliminary injunction.[21] While a federal appellate judge granted a temporary restraining order to allow a panel of three appellate judges to decide whether to grant plaintiffs’ application for an injunction pending the outcome of her suit,[22] the appellate panel denied the preliminary injunction application on September 27, 2021, allowing the city to begin enforcing the vaccine requirement on September 28, only a day after it was originally to take effect.[23]  On October 1, 2021, U.S. Supreme Court Associate Justice Sonia Sotomayor denied without explanation or statement an emergency request to enjoin the city Department of Education’s vaccine mandate.[24]  On October 12, 2021, a Southern District of New York judge similarly rejected claims that the city Department of Education’s vaccine mandate violated public school teachers’ religious rights.[25]  On November 28, 2021, the Second Circuit held that the city’s vaccine mandate was facially neutral and generally applicable, satisfying the rational basis standard of review.  The court found that imposing a vaccine mandate “was a reasonable exercise of the state’s power to protect the public health.”[26]  Nonetheless, the Second Circuit held that the vaccine mandate was unconstitutional as applied to the particular plaintiffs because the standards for determining a religious exemption required that the request for an exemption be denied if it was well documented that the head of a religious organization had spoken publicly in favor of the vaccine.  Such standards ran afoul of Supreme Court precedent that “it is not within the judicial ken to question . . . the validity of particular litigants’ interpretations” of religious creeds.[27] Because the city’s standards for determining whether an accommodation was required were not neutral, strict scrutiny applied to those standards.[28]

Mandates for other vaccinations have long existed for students. These mandates were similarly challenged by parents of children who, like the current petitioners, believed that they violated their liberty and religious rights. In Phillips v. City of New York,[29] the Second Circuit rejected a substantive due process claim brought by several parents whose children were excluded from school because they were unvaccinated, noting that the Supreme Court had, long ago, determined that states in the exercise of their police powers can mandate vaccinations when necessary to protect public health.[30] Most states, but not all,[31] statutorily grant an exemption to students who object to vaccination requirements because of sincerely held religious beliefs.  Courts have held that the First Amendment, however, does not require that they do so.[32]  In Phillips, the Second Circuit also rejected the claims of two families that were based on the Free Exercise clause, finding the mandates to be neutral and generally applicable to all students. In doing so, it quoted dicta from the United States Supreme Court in Prince v. Massachusetts[33] commenting that “the right to practice religion freely does not include the liberty to expose the community … to communicable disease ….”[34]

The religious exemption has emerged as among the most controversial issues in light of the present pandemic environment and actions taken by state and local governments to require vaccination.  Although currently “the right of free exercise does not relieve an individual of the obligation to comply with a ‘valid and neutral law of general applicability on the ground that the law proscribes (or prescribes) conduct that his religion prescribes (or proscribes),’”[35] advocates for religious freedom have been arguing that courts should strictly scrutinize any law that interferes with the practice of a religion.  The Supreme Court was asked in Fulton v. City of Philadelphia[36] to overturn Employment Div. v. Smith,[37] where it held that neutral and generally applicable laws need only be rational.  Although it declined to do so, remanding the case for other reasons in a unanimous opinion, three justices in their concurrence stated that any infringement of the free exercise of religion needed to be narrowly tailored and justified by a compelling government interest.[38] Given that opinion, and the likelihood of the Supreme Court ultimately hearing one of the cases involving a vaccine mandate, it remains to be seen whether today’s Supreme Court would follow Smith when reviewing a rule mandating that everyone, regardless of their religious beliefs, be vaccinated and conclude that such a mandate was constitutional as a rational exercise of power. Alternatively, if the Court were to overturn Smith and apply a “strict scrutiny” test, it is unclear whether it would find that the goal of containing the COVID-19 virus was a compelling government interest justifying imposition of a vaccine mandate without a religious exemption.

The public health risks posed by the pandemic have fluctuated over the past 21 months, particularly as the delta and now the omicron variants have spread.  Voluntary vaccination rates vary dramatically in different regions of the state and country and among different populations. The status of available vaccines also continues to evolve, with the U.S. Food and Drug Administration approving the Pfizer-BioNTech COVID-19 vaccine in late August[39] and more recently granting Emergency Use Authorization applications for vaccines for children under 12.[40]  State and local governments have taken a variety of actions in response to these evolving circumstances.  In response to the threat of the omicron variant, Governor Kathy Hochul issued an Executive Order on November 26, 2021, declaring a state of emergency and permitting the state’s health department to limit non-essential and non-urgent care until January 15, 2022 to protect capacity and keep beds available.[41]  The legal landscape regarding vaccine mandates also continues to change almost daily, as challenges make their way through the court system and new cases are brought. In addition, various cases have been filed seeking to invalidate New York State and New York City vaccine mandates, and more developments are expected in the weeks and months ahead.[42]

Most recently, on December 6, 2021, less than a month before the end of his tenure, New York City Mayor William de Blasio issued a broad vaccine mandate.  The mandate, effective December 27, 2021, applies to private sector workers and the City estimates it would impact roughly 184,000 businesses.  The mandate would also require proof of vaccination to partake in indoor activities, including dining, fitness and entertainment. In addition, effective December 14, 2021, the mandate requires 5-11-year-old children to get vaccinated to participate in high-risk extra-curricular activities.[43] The mandate was not authorized by the New York City Council and apparently was not coordinated with incoming Mayor Eric Adams. Legal scholar Lawrence O. Gostin wrote that the New York City mandate “could have been a model for the nation.  But it won’t because it was rushed and rammed through without consultation.”[44] The broad private sector mandate has received significant criticism from the business community and is likely to be the subject of future court challenges if Mayor-elect Adams does not vacate it. As noted, a significantly narrower federal mandate issued by OSHA has currently been enjoined.  Questions exist about the Mayor’s authority to issue such a broad mandate, particularly without authorization from the New York City Council. The city’s mandate may also be preempted by state worker safety laws.

Both for those interested in the legality of vaccine mandates and those interested in the United States Supreme Court’s First Amendment jurisprudence, the judicial response to federal, state, and local vaccine mandates bears continued watching.

Mary Beth Quaranta Morrissey, PhD, MPH, JD, is a New York health care attorney and interdisciplinary research scholar. Dr. Morrissey holds academic appointments at Fordham University’s Global Healthcare Innovation Management Center and Graduate Schools, and has recently been appointed a full-time professor at Yeshiva’s Wurzweiler School of Social Work, effective 2022. She has chaired two New York State Bar Association (NYSBA) Task Forces on issues related to the COVID pandemic, including public health legal reforms and mandatory vaccination. Morrissey also co-chairs the NYSBA Health Law Section Public Health Law Committee.

Thomas G. Merrill is an attorney who was general counsel of New York City’s Department of Health and Mental Hygiene for more than 13 years, serving four different commissioners. He is currently an adjunct professor at the City University of New York.

Christopher C. Palermo is a litigation partner at Harris Beach.  He is a member of the Executive Committee of the Food, Drug and Cosmetic Law Section of NYSBA and is the Section’s Delegate to NYSBA’s House of Delegates.

[1] Centers for Disease Control and Prevention, COVID Data Tracker, (last visited Dec. 9, 2021).

[2] BST Holdings, L.L.C. v. OSHA, No. 21-60845, 2021 U.S. App. LEXIS 33698 (5th Cir. Nov. 12, 2021).

[3] (last visited Nov. 30, 2021).

[4] Medicare and Medicaid Programs; Omnibus COVID-19 Health Care Staff Vaccination, 86 Fed. Reg. 61, 555, 61,556 (Nov. 5, 2021).

[5] Missouri v. Biden, No. 4: 21-cv-01329-MTS, 2021 U.S. Dist. LEXIS 227410, __ F.Supp. 3d __ (E.D. Mo. Nov. 29, 2021); Louisiana v. Becerra, No. 3:21-CV-03970, 2021 U.S. Dist. LEXIS 229949, __ F. Supp. 3d __ (W.D. La. Nov. 30, 2021).

[6] Louisiana, 2021 U.S. Dist. LEXIS 229949, at *2.

[7] (last opened Dec. 10, 2021).

[8] Dr. A v. Hochul, No. 1:21-CV-1009, 2021 U.S. Dist. LEXIS 199419 (N.D.N.Y. Oct. 12, 2021).

[9] We The Patriots USA, Inc. v. Hochul, No. 21-cv-4954 (E.D.N.Y. Sept. 12, 2021).

[10] We The Patriots USA, Inc. v. Hochul, Nos. 21-2178 and 21-2566, 2021 U.S. App. LEXIS 32880 (2d Cir. Nov. 4, 2021).

[11] 494 U.S. 872 (1990).

[12] We The Patriots USA, Inc. v. Hochul, 2021 U.S. App. LEXIS 32880 at *8.

[13] Id. at *45.

[14] Id. at *45-51.

[15] Id. at *51-53.

[16] We The Patriots USA, Inc. v. Hochul, Nos. 21-2178 and 21-2566, 2021 U.S. App. LEXIS 33691, __ F.4th __ (2d Cir. Nov. 12, 2021).

[17]  Id. at *3-4.

[18] John Does 1-3, et al. v. Mills, No. 21A90, 211 L.Ed.2d. 243, 595 U.S. ___ (Oct. 29, 2021).

[19] Id. at 247 (Gorsuch, J., dissenting).

[20]  (last visited Nov. 30, 2021).

[21] Maniscalco v. New York City Dep’t of Educ., No. 21-cv-5055, 2021 U.S. Dist. LEXIS 184971 (E.D.N.Y. Sept. 23, 2021).

[22] No. 21-2343, 2021 U.S. App. LEXIS 29329 (2d Cir. Sept. 24, 2021).

[23] No. 21-2343, 2021 U.S. App. LEXIS 29429 (2d Cir. Sept. 27, 2021).

[24] (last visited Nov. 30, 2021).

[25] Kane v. De Blasio, No. 1:21-CV-07863, 2021 U.S. Dist. LEXIS 210957 (S.D.N.Y. Oct. 12, 2021).

[26] Kane v. De Blasio, Nos. 21-2678 and 21-2711, 2021 U.S. App. LEXIS 35102 (2d Cir. Nov. 28, 2021).

[27] Id. at *23-24.

[28] Id. at *24.

[29] 775 F.3d 538 (2d Cir. 2015).

[30] Jacobson v. Massachusetts, 197 U.S. 11 (1905).

[31] New York eliminated its religious exemption in 2019.  Other states that have expressly repealed religious exemptions include California, Maine, Mississippi and West Virginia.

[32] See, e.g., F.F. ex rel. Y.F. v. State, 66 Misc.3d 467 (Sup. Ct. Albany Cty. 2019).

[33] 321 U.S. 158, 166-167 (1944).

[34] 775 F.3d at 543.

[35] 494 U.S. 872, 879 (1990).

[36] 141 S.Ct. 1868 (2021).

[37] 494 U.S. 872 (1990).

[38]141 S.Ct. at 1883 (Barrett, J., concurring).

[39] (last visited Oct. 6, 2021).

[40] (last visited Dec. 5, 2021).

[41] Executive Order No. 11, (last visited Dec. 10, 2021).

[42] The information contained in this article is current as of December 10, 2021. Given the ever-changing landscape in this area, it is expected that there will be additional developments in pending and new litigation in the upcoming weeks and months.

[43]“key-to-nyc-program.pdf (last visited Dec. 10, 2021).

[44] L. Gostin, “A Decent Mandate Done All Wrong: What de Blasio Got Wrong With His Vaccine Requirement for NYC Private-Sector Businesses,” New York Daily News, December 7, 2021, available at (last visited Dec. 10, 2021).

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