What Happened in the Navy SEALs Vaccine Mandate Lawsuit Against the Biden Administration?

The Big Picture

Before being sworn into office, President-elect Biden said that COVID vaccines should not be mandatory, and he “wouldn’t demand it to be mandatory.” That was December 2020. Since that pronouncement, the Biden Administration has done the exact opposite.

In November 2021, the Occupational Health and Safety Administration (OSHA) announced its vaccine or test mandate. Under that mandate, employers with 100 or more employees were required to check each employee’s vaccination status, and keep a record of it on file. If the employees were not vaccinated, they had to take a weekly test that they paid for and were required to wear a mask in the office. Employers that violated the mandate could be fined up to $13,653 for a standard violation, and up to $136,532 for a willful one. In late January, the Supreme Court held OSHA had likely exceeded its statutory authority. As a result, OSHA rescinded its mandate.

In November 2021, the Department of Health and Human Services (HHS) issued a final rule that facilities that participate in Medicaid and Medicare programs were required to have their staff vaccinated. Unlike OSHA’s vaccine or test mandate, HHS’s rule was truly a vaccine mandate. Facilities that chose to keep unvaccinated employees, contractors, or volunteers on staff would lose all federal funds and be terminated from the programs. With this mandate, the government essentially required the vaccine for 10 million Americans. In late January, the Supreme Court held that the Biden Administration’s rule was legal under a series of statutes.

In September 2021, President Biden signed Executive Order 14042 that directs executive departments and agencies to ensure that their contracts and subcontracts include a clause requiring contractors and subcontractors to comply with guidance published by the Safer Federal Workforce Task Force. In late September, the guidance specified that any employee of a prime contractor or subcontractor must be vaccinated. Again, unlike OSHA’s mandate, there is no testing option. Several federal courts have enjoined (prohibited) the Biden Administration from enforcing the mandate. Most notably, the 11th Circuit refused to lift a district court’s nationwide injunction (an injunction that applies across the entire country, not just to the parties in the case).

Finally, in late August 2021, Secretary of Defense Lloyd Austin released a memorandum requiring “full vaccination of all members of the Armed Forces under DOD authority on active duty or in the Ready Reserve…” In November, the Navy released guidance that if any servicemember had not received one shot of the COVID vaccine by November 28th, he or she would receive a general discharge. As a result, 26 Navy SEALs and 9 Navy servicemembers sued claiming the mandate violated their religious beliefs. In early January, a Federal District Court agreed and enjoined the government from enforcing the mandate.

The Details

  • Of active-duty Navy servicemembers, 99.4 percent are fully vaccinated. The plaintiffs represent the remaining 0.6 percent. The Navy has denied 29 of the 35 accommodation requests, some of which have been appealed internally. See pages 3-4.
  • The Navy’s policy allows for three exemptions: (1) medical, (2) those who participated in on-going COVID clinical trials, and (3) religious. However, the Navy has not granted a religious exemption for a vaccination in seven years. See page 3.
  • The mandate treats medical exemptions more favorably than religious exemptions. If a medical exemption is granted, that servicemember is still deployable. If a religious exemption is granted, that servicemember is nondeployable and is medically disqualified from becoming deployable. To become deployable, the servicemember must seek a medical waiver. See page 3 and 14.
  • The religious accommodations process is a six-phase, fifty-step process. At phase one, an administrator updates a prepared disapproval template with the requester’s name and rank. See page 4.
  • After the disapproval letter is written, it is sent to seven offices to review. After the offices review the letter, the administrator prepares an internal memo to Vice Admiral John Nowell asking him to sign the letter disapproving the religious exemption. See page 10.
  • At step 35 the administrator is told to read the religious accommodation request for the first time, even though the disapproval letter has already been written, the disapproval letter has been reviewed by several officers, and an internal memo signed by the Vice Admiral denying the exemption has been drafted. At no point in the process is the administrator given the opportunity to recommend anything other than disapproval. See pages 10-11.
  • To date, the Navy has never accepted a religious accommodation while it has accepted several medical exemptions. See page 14.
  • Senator Ted Cruz led an amicus brief with 9 U.S. Senators and 38 members of the House of Representatives arguing in favor of the Navy servicemembers.


Before reaching whether the servicemembers were likely to succeed on the merits, there were two threshold issues the court considered. First, the court concluded that President Biden needed to be dismissed from the case because it had no declaratory or injunctive power over him. Second, the court considered whether it could hear the case because the servicemembers had not exhausted all their military remedies. Because the record showed the Navy’s accommodation process was “an exercise in futility” and the questions presented were constitutional ones and did not involve military expertise, the court held it could hear the case.

The servicemembers brought two claims. First, under the Religious Freedom Restoration Act (RFRA), the court held they were likely to succeed because the Navy could not demonstrate a compelling interest in vaccinating the remaining 0.6 percent of servicemembers. Second, under the First Amendment’s Free Exercise Clause, the court held they were likely to succeed because the Navy’s mandate is not neutral and generally applicable, and it failed strict scrutiny. It allows for individualized exemptions and treats secular conduct better than religious conduct because it allows servicemembers with medical exemptions to still be deployable, while those with religious exemptions are medically disqualified from being deployed. As a result, the court placed an injunction prohibiting the Navy from enforcing its policy against these servicemembers.

Constitutional Law Background

The First Amendment provides that Congress shall pass no law…prohibiting the free exercise of religion. See U.S. Const. amend. I. To enforce this and other constitutional rights, the Supreme Court (Court) has developed a series of tests or standards of review that apply in different factual situations. The factual situation relevant in this case is when the government takes an action through a law or regulation that burdens someone’s sincerely held religious beliefs. In this case, the servicemembers argue that the government has burdened their religious beliefs because they oppose the use of aborted fetal cell lines in the development of the vaccine, among other reasons. As a result, if the servicemembers do not take the vaccine, which they argue goes against their sincerely held religious beliefs, they will be fired.

After a challenger shows government action burdens their sincerely held religious beliefs, the next question is what standard of review applies? The traditional test comes from a case called Employment Division v. Smith (1990). There, the Court held that government actions that burden religious conduct but are neutral and generally applicable are constitutional. If a challenger shows the government action is not neutral or generally applicable, a standard of review known as strict scrutiny applies. When strict scrutiny applies, the government almost always loses.

Traditionally, a challenger has a difficult time proving the government’s action is not neutral. If the object or purpose of the law is to infringe on or restrict religious practice because of their religious motivation, the law will fail neutrality. But most laws or regulations are likely not enacted with religious animus, and even if some are, it is difficult to prove. Challengers can also try to show a lack of neutrality through circumstantial evidence based on the background of the decision, the series of events that led to enactment, or other legislative or administrative history that includes statements made by members of the decision-making body. Lack of neutrality is often not why the government loses under the Free Exercise Clause.

The most prominent case where the Court found lack of neutrality was Masterpiece Cakeshop v. Colorado Civil Rights Commission (2018). In Colorado, complaints under its anti-discrimination statute are first addressed with the Colorado Civil Rights Commission (Commission). While the Commission considered Phillip’s case, the commissioners made a series of comments at a public hearing that showed hostility toward Phillip’s faith. At a later meeting, a commissioner described “freedom of religion” as “one of the most despicable pieces of rhetoric that people can use,” and compared Phillip’s defending the sincerity of his faith to defenses of slavery and the holocaust. Not a single commissioner objected to these comments. While there were a few other facts that also showed a failure of neutrality, the point is these cases do not happen often.

Since Smith, almost every victory under the Free Exercise Clause happens because the government’s law or regulation is not generally applicable. The government usually fails general applicability in one of two ways. First, the government provides a series of individualized exemptions, but does not extend an exemption to cases of religious hardship. Or, the government prohibits religious conduct, but allows secular conduct that undermines the government’s interest in a similar way.

Fulton v. City of Philadelphia (2021) is an illustration of the first and usual way the government fails general applicability. In Fulton, Catholic Social Services (CSS) and Philadelphia had a contract that stipulated that the city would refer foster children to CSS for placement with families. When Philadelphia learned CSS would not certify same-sex couples to be foster parents because of its religious beliefs about marriage, the city stopped referring children. Philadelphia argued CSS violated the contract because of a provision that prohibited providers from rejecting foster or adoptive parents based on their sexual orientation. However, the contract also stipulated that the Commissioner or the Commissioner’s designee could grant an exception from the prohibition in his or her sole discretion. In other words, the policy was not generally applicable because Philadelphia allowed exceptions from its prohibition but did not extend an exception to CSS’s case of religious hardship.

However, the Court’s neutrality and general applicability doctrine has not always been clear. Throughout the COVID pandemic, state and local governments imposed stricter gathering limits on churches and synagogues than other businesses. At one point, New York imposed a rule that churches or synagogues in “red zones” could not admit more than 10 people. However, businesses categorized as “essential” like acupuncture facilities, grocery stores, hardware stores, liquor stores, bicycle repair shops had no capacity restrictions. From these facts, the Court explained that government action is neither neutral nor generally applicable whenever it treats secular conduct more favorably than religious conduct. See Roman Catholic Diocese Of Brooklyn v. Cuomo (2020).

Under Smith, if a government’s action is not neutral or generally applicable, strict scrutiny applies. It is debatably the hardest test in constitutional law, and when it is applied correctly, the government usually loses. The government must show it has a compelling government interest, and the law or regulation is narrowly tailored in pursuit of that interest. Moreover, the government must also show its action is the least restrictive means of achieving the compelling interest. In other words, if there are other ways the government could achieve its goals that have less of a burden on religious conduct, the government loses. “A law that targets religious conduct for distinctive treatment or advances legitimate governmental interests only against conduct with a religious motivation will survive strict scrutiny only in rare cases.” See Church of the Lukumi Babalu Aye, Inc. v. Hialeah (1993).

Smith represented a sea change in constitutional law. Before Smith, courts would review Free Exercise challenges with something like strict scrutiny regardless of whether the government’s action was neutral or generally applicable. In response to Smith, bipartisan majorities in Congress passed and President Clinton signed into law RFRA. Under RFRA, Congress attempted to reinstate the pre-Smith test. RFRA originally applied strict scrutiny to any government’s action—federal, state, and local. However, in City of Boerne v. Flores (1997), the Court held that RFRA was unconstitutional as applied to state and local governments because Congress had exceeded the scope of its authority under § 5 of the 14th Amendment. In sum, strict scrutiny applies only whenever the federal government imposes a burden on religious conduct.

Claim #1: The Religious Freedom Restoration Act

Under RFRA, the government can substantially burden a person’s free exercise only if it shows “that the application of the burden to the person—(1) is in furtherance of a compelling governmental interest; and (2) is the least restrictive means of furthering that compelling governmental interest.” See 42 U.S.C. § 2000bb–1(b). While some might think the military might not be covered under RFRA, the definition of government includes “a branch, department, agency…” See Id. § 2000bb–2(1). As stated above, this is the strict scrutiny standard of review.

The main point of contention was whether the Navy had a compelling interest in vaccinating these servicemembers. The Navy argued that slowing the spread of COVID is a compelling interest, a point the Supreme Court has made before, and that the Navy must have a healthy force that is ready to deploy at any time. Moreover, because these servicemembers are members of Special Operations teams, they need to be healthy to carry out their specific missions. In response, the servicemembers argued the government does not have a compelling interest in vaccinating these servicemembers two years into the COVID pandemic.

The court noted that throughout the pandemic, these servicemembers have performed their jobs well. In addition, some of them have conducted large-scale trainings while others have successfully deployed. With respect to one servicemember, the Navy awarded the Joint Service Commendation Medal for “safely navigating restricted movement and distancing requirements” under the COVID protocol in 2020.

The fact that took the case over the top was that 99.4 percent of all active-duty Navy servicemembers are vaccinated, and the 35 remaining are highly unlikely to undermine the Navy’s effort. Moreover, some of the servicemembers had COVID previously and tested positive for antibodies. Further undermining the Navy’s alleged compelling interest was the allowance of servicemembers with medical exemptions, allergies to the vaccine, or those who were in a COVID vaccine trial to still be deployable. Like the servicemembers seeking a religious exemption, those servicemembers could be deployed and catch COVID just as easily. In sum, the Navy failed to demonstrate a compelling interest, and the Court held the servicemembers were likely to succeed on their RFRA claim.

Claim #2: The First Amendment’s Free Exercise Clause

As stated above, the first question in a Free Exercise analysis comes from Smith, and that question is whether the government’s action is neutral and generally applicable. The court held the mandate was not neutral or generally applicable. First, the mandate failed general applicability because it allowed for individualized exemptions. But, while the Navy claims to allow for religious exemptions, it has never granted one. Second, the mandate failed neutrality because it treats secular conduct more favorably than religious conduct. Servicemembers granted a medical exemption are still deployable while servicemembers granted a religious exemption are medically disqualified, and not deployable unless they seek and are granted a medical waiver.

The Navy defended treating medical exemptions more favorably than religious exemptions because the number of servicemembers seeking religious exemptions far exceeded those seeking medical exemptions. However, regardless of the number of servicemembers seeking to vindicate their First Amendment rights, the policy still treats secular conduct more favorably than religious conduct.

Because the mandate was not neutral or generally applicable, the Navy had to meet strict scrutiny. However, as noted in the RFRA analysis, the Navy did not have a compelling interest in vaccinating these 35 servicemembers and could not meet strict scrutiny. The court held the servicemembers were likely to succeed on their First Amendment claim.

What Happens Next?

The Navy has appealed the court’s preliminary injunction to the 5th Circuit Court of Appeals. The issues presented here might ultimately be worthy of Supreme Court review. To date, the Court has rejected several vaccine mandate cases where plaintiffs brought First Amendment Free Exercise claims. Most prominently, the Court denied review in New York and Maine.