President Biden’s sweeping mandate to vaccinate millions of federal workers and contractors against the coronavirus left officials confronting how to carry it out amid a fusillade of workplace rules that could complicate — and lengthen — the process and further upend a government struggling to return to normal.

The often-arcane labor rules governing the country’s largest employer could have the effect of allowing thousands of civil servants who are expected to refuse a vaccine to be paid to stay home — not working — while their cases are adjudicated, raising thorny questions about rewards for intransigence.

The president’s most aggressive action yet to protect government workers from the virus and offer a model to the country’s other employers came less than six weeks after a separate order telling 2.1 million civilian federal employees to get vaccinated or face repeated testing. But that plan was beset by challenges and had barely begun to roll out at many agencies, according to multiple federal officials.

As some union officials reflected opposition to Biden’s plan, other workers raised the possibility that vaccine-hesitant employees who are close to retirement — there are hundreds of thousands nearing that point — could decide to put in their papers early.

“There’s a great deal of concern about how this will play out,” said Chad Hooper, executive director of the Professional Managers Association, which represents managers at the Internal Revenue Service, where about two-thirds of employees are still working from home.

Part of the challenge facing managers, employees and the unions that represent them is what they don’t know.

On Friday, White House officials on the coronavirus task force faced anxious questions on a call with managers and unions on the front lines of carrying out the mandate, with many raising concerns about discipline for employees who refuse shots, managers’ expertise and bandwidth to review requests for exemptions and record-keeping required to monitor employees’ vaccine status, according to two participants.

The executive order the White House issued Thursday offers few details, but the coronavirus task force said it plans to issue guidance to agencies within the next week. Meanwhile, the continued threat posed by the highly contagious delta variant continues to thwart the administration’s plan — originally scheduled to start Oct. 1 — to bring large swaths of the government now teleworking back to the office to resume normal operations.

The federal workers mandate, part of a larger rollout of measures to quell the coronavirus that also reached into the private sector, requires most executive branch employees and companies that do business with the federal government to get shots. The policy applies to hundreds of thousands of employees now working from home, as well as those who have returned to their offices or never left.

More than 2 million active duty service members and civilian federal workers at the Defense Department, Veterans Affairs, the Indian Health Service and other agencies — many of them health-care providers — had already received vaccine mandates this summer.

The U.S. Postal Service has not issued a vaccine requirement for its workforce of almost 650,000, but the administration said that postal workers will be covered under a new Labor Department rule Biden announced Thursday directing employers with more than 100 workers to get their staff vaccinated or require weekly coronavirus testing.

White House press secretary Jen Psaki said Thursday that federal employees will be given “about 75 days” to become fully vaccinated. The mandate will have “limited exceptions” for medical or religious reasons, she said. Employees who refuse to comply will face disciplinary action that is likely to vary among agencies, depending on what is laid out in their collective-bargaining agreements. Union officials said they hope any discipline to start with written warnings and progress to suspensions without pay — and possible dismissals.

Psaki said federal employees will “go through the standard HR process, which includes counseling, and face disciplinary action — face progressive disciplinary action” if they refuse to get vaccinated and do not qualify for medical or religious exemptions.

“[Hopefully] it doesn’t come to [termination], but our role is of course to convey to federal employees the safety, effectiveness, and the availability of vaccines.”

The government does not collect centralized data on employees’ vaccine status. There is widespread agreement, however, that the workforce — of which 85 percent is outside of Washington — reflects national trends, which show that about 75 percent of adults over 18 have received at least one shot.

In a recent Washington Post-ABC news poll, about 7 in 10 unvaccinated workers who were not self-employed said they would probably quit if their employer required them to be vaccinated and did not grant a medical or religious exemption.

The numbers who have received or are open to seeking vaccines are lower in conservative areas — and that is largely where agencies expect to face objections or find employees quitting outright.

“The people who haven’t been vaccinated yet are going to stay that way,” said James Shanahan, secretary/treasurer of the American Federation of Government Employees Local 45, which represents about 650 Agriculture Department food inspectors in Nebraska, Iowa, Kansas and Missouri. “I believe the federal government is going to lose some employees over this.”

Shanahan said that while he is “100 percent vaccinated,” he is not sure he wants to tell his agency his status in writing out of concern that his privacy won’t be protected. He is six months from retirement, he said, and there’s a chance he will retire over the mandate.

“You hate to stand on principle,” he said, “but a lot of people will do that.”

Larry Cosme, president of the Federal Law Enforcement Officers Association, said in a statement that the mandates were “misguided.”

“We understand that threatening people’s livelihood and penalizing employees for making independent medical decisions is not the answer,” he wrote.

The first coronavirus plan for most federal employees, announced at the end of July, required employees to “attest” to their status and threatened discipline only if someone was discovered to have lied about their vaccination status. But little was done to push that plan along before Thursday’s was announced.

“The attestation [phase] failed,” said Jason Briefel, partner at Shaw Bransford & Roth, who represents several federal employee associations, including the Senior Executives Association, which represents about 1,700 career senior leaders in government. “There were templates, there was guidance, but it appears there’s a major disconnect between the center of government and [agencies’] ability to navigate this change on the ground.”

“We did not feel the ‘throw it over the fence to the agencies’ strategy was the right one,” Briefel said.

The Treasury Department, for example, planned to start testing only in mid-October, Hooper said. The White House budget office had promised agencies that it would provide access to a contractor, but not until late fall.

Most officials agree that a mandate will be more simple to implement than the earlier policy. But if the traditional system for punishing employees is used for those refusing vaccines, as Psaki suggested, another raft of complications would come into play.

The administration, in guidance to agencies sent in August after the first vaccine plan was announced, said that employees who refused to get tested could be placed on administrative leave, a form of paid time off used widely for short-term absences. It is also used when a manager proposes removing an employee, with final action within 30 days.

But in recent years, the policy was widely considered to have been abused by managers who wanted to sideline troublesome workers while misconduct or poor performance reports were adjudicated. Managers were often slow to respond to employees’ responses to proposed removals and to issue final removal notices, so the process dragged out.

Congress, intending to curb abuses, passed a law in late 2016 that severely restricted the use of paid leave. But the Office of Personnel Management did not issue regulations to implement it, so managers still have wide latitude to use paid leave for long periods.

The OPM rule book lists dozens of reasons for allowing paid leave, such as donating an organ, house-hunting before a job transfer and attending the funeral of a relative in the military. Some employees remain on paid leave while they challenge demotions and other punishments.

“What’s the incentive for someone to get vaccinated, who doesn’t want to do it, when they could get a paid vacation?” asked Todd Wells, executive director of the Federal Managers Association, which represents 200,000 managers and senior executives across the government, many in national security roles. He cited naval shipyards that rely on thousands of employees to maintain vessels round-the-clock.” We’re trying to literally keep the ships running and you’re saying, go home for a few months and take a vacation.”

Cathie McQuisten, deputy general counsel for the American Federation of Government Employees, the largest federal employee union with 700,000 members, said that employees were entitled to due process. She said she expects that any move to discipline or fire employees who do not comply with the mandate would not start until “day 76” of the grace period to get shots.

“My understanding is that before that, you’re not in violation,” she said.

Some mandates that took effect at government agencies this summer have shown early success at boosting vaccinations, officials said. In the seven weeks since Veterans Affairs rolled out a mandate for its front line health-care workers, 82 percent now have shots, up from 77 percent, spokesman Terrence Hayes said.