With a Monday deadline looming, high percentages of federal workers are reporting they have been vaccinated against the coronavirus. But tens of thousands of holdouts have requested exemptions on religious grounds, complicating President Biden’s sweeping mandate to get the country’s largest employer back to normal operations.

Federal agencies have yet to act on the requests piling into managers’ inboxes from vaccine resisters seeking accommodations that would allow them to continue their jobs unvaccinated rather than face the possibility of being fired as the administration has threatened. A far smaller number of employees have asked for exemptions on medical grounds, officials said, prompting what are likely to be more clear-cut decisions on whether to grant them.

The number of religious objectors ranges from a little more than 60 people at the Education Department to many thousands among the 38,000-strong workforce at the Bureau of Prisons, according to federal employee union officials.

A Texas-based IRS affinity group, Christian Fundamentalist Internal Revenue Employees, wrote a four-page letter to the official handling exemption requests, citing scripture and mistrust of the government among African Americans, as well as falsely claiming thousands of deaths from the coronavirus vaccine.

The letter questioned whether granting exemptions would pose any undue hardship, citing the agency’s widespread use of telework during the pandemic. “The IRS already has accommodations in place to meet the requests and still accomplish their mission to the taxpayer,” Lorenzo Henry, the group’s national president, wrote.

Exemption requests have become the go-to alternative for those opposed to coronavirus vaccines because managers must hold off on discipline while requests are reviewed. With a Nov. 22 deadline for employees to show proof of full vaccination status, Monday is the deadline to get a Johnson & Johnson shot or a second dose of the Pfizer or Moderna vaccine.

The process could take months for officials designated at each agency, leaving anxious employees in limbo and delaying implementation of a mandate Biden announced in September as a model for employers nationwide. The administration saw the vaccine program as essential to getting workers back in their offices and improving services to taxpayers.

How to fairly and legally weigh the surging requests and determine who receives an exemption has consumed federal attorneys, the Equal Employment Opportunity Commission (EEOC), unions and outside lawyers helping employees with the process. The deliberations are particularly acute as the government tries to balance the right to religious freedom against the goal of creating safe workplaces for 2.1 million civilian employees.

Managers will soon assume the thorny role of deciding whether someone is sincere or requesting an exemption for political reasons. In a directive issued in January, the EEOC said the objections do not have to stem from an organized religion and can be beliefs that are new, uncommon or “seem illogical or unreasonable to others.”

Kevin Owen, a partner at Gilbert Employment Law in Maryland, said he has heard from more than 100 federal employees pursuing religious and medical exemptions to the vaccine mandate.

“The case law is well-developed for disabilities,” Owen said. “Agencies have not hired new H.R. specialists to deal with the religious requests, and a lot of them do not have clear guidance yet on how to proceed.”

Officials estimate that most unvaccinated employees who have not quit or retired by this point are seeking an exemption. The IRS informed its employees in an email Wednesday that unvaccinated people should expect counseling letters, followed after Nov. 23 by proposed suspensions and removals beginning in December for those still not in compliance.

Under federal workplace rules, those awaiting word on an exemption cannot be summarily fired, and it is unclear how agencies plan to safeguard vaccinated colleagues in the meantime in what typically are close quarters.

Courts and municipal governments are also adjudicating these questions as unvaccinated police officers, health-care workers and others in essential roles challenge vaccine mandates. Exemption requests could grow in the private sector, too, following last week’s Labor Department rule requiring companies with 100 or more employees to have their workers fully vaccinated or face weekly testing and masking. (That action was temporarily suspended Saturday by a panel of appellate judges, who did not rule on the merits of the policy.)

Jeffrey Zients, the White House’s covid response coordinator, said this week that religious exemptions have existed for past vaccines and pledged that federal agencies “are following rigorous processes to evaluate religious and medical exemptions.”

But the government has never faced anything on the scale of the coronavirus pandemic as it attempts to stand up a coast-to-coast vaccine mandate with a politicized, contagious disease still spreading, large swaths of the workforce seeking a way out and potentially dire effects on day-to-day operations if employees are fired for noncompliance in large numbers.

“These aren’t typical accommodation requests like giving someone an ergonomic chair,” said Cathie McQuiston, deputy general counsel for the American Federation of Government Employees, the largest federal employee union, with 700,000 members. “It’s not just about the employee, but the impact on co-workers and their right to a safe workplace, and agencies have to be consistent.”

If a request is turned down, the employee must decide whether to get vaccinated or risk losing their job. If the request is granted, the unvaccinated worker must wear a mask, socially distance at the office and be tested regularly. The administration has not yet said who will pay for those tests or where they will be administered. Even with much of the government still working from home because of the pandemic, telework is not supposed to be an approved excuse for being unvaccinated.

The Biden administration has been reluctant to offer many details about how its program is progressing. The Washington Post asked 10 civilian agencies for information on their vaccine rates and exemption requests as of last week; nine either did not respond or declined to disclose them. The agencies issued identical statements that said they were “laser-focused on vaccinating their workforce” by Nov. 22, at which point the administration says it will make more information public. Agencies have set different deadlines for employees to submit exemption requests, with most Nov. 22 or sooner.

“We are confident in the ongoing implementation of vaccination requirements across the federal government,” said Isabel Aldunate, spokeswoman for the Office of Management and Budget, which is overseeing implementation of the mandate with the agencies. “Our strategy is working and will help ensure the health and safety of the entire federal workforce.”

Agency and union officials, some speaking on the condition of anonymity to disclose private figures, cited rates that varied in both directions from national statistics showing that just under 70 percent of adults have received at least one shot and about 58 percent are fully vaccinated.

The Bureau of Prisons was well below national rates, with just 58 percent of its workforce at least partly vaccinated, and the Transportation Security Administration was at about 60 percent, according to the most recent data, officials said.

Higher rates were found at Veterans Affairs, the first agency to impose a mandate, where 76 percent of the 420,000 employees were fully vaccinated, according to the agency’s website. At the Environmental Protection Agency, 81 percent had been fully vaccinated by last week, and the rate was 78 percent at the IRS in mid-October.

The Defense Department, the largest federal agency, with nearly 840,000 employees, said 45 percent of its civilian workforce had received at least one dose. The Air Force, which imposed the most aggressive timeline in the military to immunize all active-duty personnel, reported that about 97 percent received at least one dose by its Nov. 2 deadline, leaving just more than 8,400 unvaccinated.

An additional 1,634 have received medical exemptions, but a vast majority are temporary, said Ann Stefanek, an Air Force spokeswoman. Temporary medical exemptions are issued for circumstances such as someone with a current coronavirus infection waiting for a doctor to authorize a vaccination.

Defense officials said permanent vaccination exemptions historically have been rare for the military, which requires troops to receive other vaccinations. The Navy has granted only six permanent medical exemptions ahead of its deadline for active sailors on Nov. 28, officials said. The active-duty Army, which faces a Dec. 15 deadline, has approved one for medical reasons.

Exemptions on religious grounds have been rare, as well, but nonetheless close to 5,000 Air Force members have submitted requests to avoid a coronavirus vaccination, with no approvals reported as of last week.

At the IRS, 2,000 of roughly 70,000 employees had filed exemption requests as of mid-October, with the vast majority of them for religious reasons, according to the Professional Managers Association, which represents agency managers. The General Services Administration received about 1,000 requests for religious and medical exemptions, an attorney familiar with the number said, and TSA officials were expecting theirs to number in the thousands in a workforce of 65,000.

At Veterans Affairs, Secretary Denis McDonough said last month that the number of religious objections was greater than the exemptions granted to resisters to the Veterans Health Administration’s year-old mandate for an annual flu shot, which amounted to more than 21,000 employees.

Employees do not need to provide proof of a religious conviction to justify a claim, only having to attest that their religious beliefs are “sincerely held.” The federal Civil Rights Act of 1964 requires employers to provide “reasonable accommodation” for those who object to a job requirement based on their faith.

The EEOC said in its directive that the sincerity of an employee’s stated religious belief usually is not in dispute. Experts in civil rights law said an agency’s decision will come down to an employee’s credibility. Some managers are asking whether employees received vaccinations for other illnesses such as the flu, officials said.

Instead of parsing motives, personnel officials are likely to consider whether an unvaccinated employee creates an “undue hardship” on the government and, if so, deny a request.

At Veterans Affairs, McDonough said that while it will not “question the legitimacy of any employees’s religious exemption,” the agency will dismiss someone when “an unvaccinated employee poses a risk to the health of our veterans. . . . This would present an undue hardship to us and ultimately to the veteran.”

The union representing the Bureau of Prisons employees has urged those who do not want a vaccination to request an accommodation.

“A very big majority are religious,” said Brandy Moore, national secretary-treasurer of the Council of Prisons Locals 33 of AFGE, which represents about 30,000 of the agency’s 38,000 employees. “These people are like, ‘I’m strongly against abortion, how can you force me to get this?’ ” (Coronavirus vaccines do not contain actual fetal cells. Decades-old fetal cell lines were used in some aspects of vaccine testing and development, as they have been for other vaccines.)

Opposition to shots within the federal prison system is so widespread that on one day last month, 62 of 350 employees at the FCI Jesup prison in southern Georgia filed for religious exemptions, union officials said.

As the TSA scrambled to secure early access to coronavirus vaccines for its screening officers this spring, Drew Rhoades stepped up to help organize the effort. But Rhoades, a manager in Minnesota, is refusing to get the shot himself, saying in his exemption request that it would conflict with his Christian Science faith, which generally eschews medicine in favor of religious healing.

“I rely on God,” Rhoades said. “I rely on prayer.” He said he would rather resign than get the shot but later added he would fight in court if he lost his job.

TSA Administrator David Pekoske told employees at a town hall this week that he expects thousands of formal objections. He encouraged employees to get vaccinated or to seek an accommodation if they believed they had grounds for one.

“Don’t hesitate to submit that exemption request,” he said.

Pekoske acknowledged that the reviews “could take weeks and weeks to work through.”

The timing could put the TSA on uncertain footing as it plans for a surge in holiday travel amid ongoing struggles to fill its ranks in a tight labor market.