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Two months after the Biden administration’s deadline for federal workers to be vaccinated against coronavirus so they could begin returning to the office, the government’s plan to resume normal operations remains muddled.

Even before a federal judge in Texas issued a preliminary injunction Friday blocking President Joe Biden’s vaccine mandate for the workforce of 2.1 million, many agencies had not mapped out when to bring employees back and how to keep them safe.

About half the workforce is still working from home nearly two years into the public health crisis, after soaring omicron cases prompted agencies to scrap return-to-office plans intended to kick in after the new year. Most employees have no idea when they’ll be back.

And while the vast majority of the civilian workforce is vaccinated — a victory for the administration — tens of thousands of employees are not. They are still inspecting meat, working airport security X-ray machines, guarding federal prisoners, tending to sick veterans and serving the public directly in other ways — some with testing requirements, some not — while decisions about protecting their colleagues and the public drag on in agency-by-agency negotiations.

Officials say they’re still contemplating how they’ll deal with unvaccinated employees while keeping vaccinated colleagues and the public safe — whether by reshuffling jobs, sending unprotected staff home to work or reconfiguring offices to keep them at a distance.

Even a coronavirus testing program for those employees exempted from the president’s vaccine mandate won’t begin for another month, after a similar testing effort last summer failed to get off the ground.

“We’re at a point in the pandemic when all the processes are out the window,” said Chad Hooper, executive director of the nonprofit Professional Managers Association, which represents managers at the Internal Revenue Service, whose leaders recently warned the public to expect subpar service this tax season. “Why is every function of the federal government having to develop a strategy independent of the other?”

Some agencies have announced return-to-office plans that will still allow large swaths of their staffs to continue to telework a few days a week. The plans could change if virus transmission is high in certain areas of the country.

Housing and Urban Development employees are scheduled to return March 14. The Environmental Protection Agency will require political appointees and high-level managers to begin going back Feb. 28, with another wave to phase in March 28, but there’s no word yet on rank-and-file employees.

The Social Security Administration, under intense pressure for months from Congress and advocates for the disabled to reopen its vast network of field offices, is scheduled to begin in-person service there in April. The administrative law judges who hear appeals of denied claims for disability benefits — and are now conducting hearings on the phone or through videoconferencing — will resume in-person work in May and June, the agency said last week.

Other agencies are still negotiating over their returns, with the biggest hurdle finding agreement with unions, which must get 30 days’ notice before employees return and have generally pushed for more time working from home.

“The Federal Government’s implementation of vaccination requirements for Federal employees has been an unequivocal success that has increased vaccination, saved lives, protected our workforce, and strengthened our ability to serve the American people,” Isabel Aldunate, spokeswoman for the Office of Management and Budget, which is overseeing federal coronavirus policy, said in an email. She did not address specifics of the return plans.

The Texas ruling came four months after the White House announced that more than 3.5 million civilian employees and military personnel would be required to get vaccinated by Nov. 22. The mandate did not offer an option for them to be tested regularly instead, except for those granted waivers. As of December, 92.5% of federal workers had received at least one vaccine dose and another 5.5% had requested medical or religious exemptions, according to OMB.

Millions of contract employees who do business with the government face additional uncertainty: This month’s Supreme Court ruling blocking the administration’s vaccine-or-test rule for private companies left contractors to decide whether to backtrack on vaccine requirements and testing or keep in place their own mandates. Many also will have to comply with a hodgepodge of state and local policies.

Still pending is the Biden administration’s appeal of a ruling by a federal judge in Georgia that halted a White House requirement for vaccine mandates to be rolled into new federal contracts. On top of that, federal buildings have varying pandemic rules governing access by civilians and contract employees.

“It’s pretty hard when some people have to comply [with vaccine rules] and others don’t,” said David Berteau, president and CEO of the Professional Services Council, which represents about 400 federal contractors who employ hundreds of thousands of people around the country and abroad.”You can imagine what companies are going through trying to make sense of all of this.”

The government’s sheer size, as well as required union negotiations and due process requirements before any penalties for noncompliance are meted out, have added more complexity.

“We’re in this fuzzy phase right now on unvaccinated employees, and omicron has allowed agencies to hit pause on figuring that out,” said Nicole Cantello, an attorney at the Environmental Protection Agency who is president of Chicago-based Local 704 of the American Federation of Government Employees.

Holdouts have responded to the threat of discipline with increased vaccinations. But unvaccinated rates are higher in conservative areas of the country, including a significant share of the staff at agencies such as Veterans Affairs (11.5%); Agriculture (11.8%); Energy (9%); the Bureau of Prisons (17.5%); Homeland Security (10.5%) and Social Security (9.7%).

The administration said last fall that it would discipline and potentially dismiss holdouts, unless they received exemptions.

But discipline has been largely limited so far to “counseling” to coax compliance and to short suspensions, according to government officials. Agencies say they’re still sorting through tens of thousands of waiver requests, the majority on religious grounds, a process VA Secretary Denis McDonough last week acknowledged is moving slowly at his agency.

“The goal is shots in arms,” McDonough said. Of disciplinary measures, he added, “I’m not in any rush to execute this.”

He said VA does not intend to question the legitimacy of either medical or religious exemption requests and plans to grant them, allowing unvaccinated employees to wear masks, socially distance and be tested regularly. In some health care settings, including nursing homes, cancer and spinal cord injury wards, employees could still lose their jobs, McDonough said, although that has not happened.

Other officials, who spoke on the condition of anonymity to discuss personnel decisions, say they also do not envision firing hundreds or even thousands of employees in their agencies, but are leaning toward granting waivers.

About 7,000 of 36,000 employees of the federal prison system have requested religious or medical waivers, Bureau of Prisons spokeswoman Kristie Breshears said. The agency has made rulings in half the cases. Breshears declined to say how many were granted or denied.

The bureau “is committed to ensuring the safety and security of all inmates in our population, our staff, and the public” and requires unvaccinated staff to test, wash hands, wear masks and employ social distancing, Breshears wrote in an email.

Unvaccinated federal air marshals could soon face real repercussions. The Transportation Security Administration determined in December that marshals could generally not be granted religious accommodations in part because of the barriers their status poses to international travel, a requirement of the job. Some countries limit entry to vaccinated travelers, and the Centers for Disease Control and Prevention advises the unvaccinated to quarantine after returning from overseas.

Instead, according to an agency memo obtained by The Washington Post, marshals will be able to transfer into different roles at the same or lower pay or be subject to “nondisciplinary removal.” To date, no marshals have been reassigned, TSA spokesman R. Carter Langston said.

The TSA said Friday it had 3,000 employees with active COVID cases, roughly double the figure at the beginning of the year. It has closed some checkpoints in at least one airport but says the impacts have been minimal.

About 5,500 employees across TSA sought waivers as of December, according to a memo signed by Administrator David Pekoske. Panels of senior staff are evaluating the requests, Langston said. Another 3.8% of the staff that has neither sought waivers nor been vaccinated have received letters of counseling but no further discipline.

The Department of Defense, with the largest civilian workforce of about 760,000, has started its exemption process, spokesman Army Maj. Charlie Dietz said. The department is not yet ready to provide initial numbers of requests, he said.

Uniformed service members have faced swifter action for vaccine refusal. About 3,000 soldiers had received letters of reprimand as of Jan. 11, the Army said, which in many cases will halt careers and in other cases will ultimately end them. The Marine Corps has discharged 334 Marines for vaccine refusal and the Air Force has ushered out 100 airmen, the services have said.

The Marine Corps recently approved two religious accommodation requests, the first among service members in the Defense Department. Thousands of troops have requested exemptions but only a handful have been approved, with officials citing a need to balance religious and medical accommodations with mission requirements.

The Agriculture Department is balancing calls to vaccinate with a recognition that its workforce and its constituents live largely in red states, where many object to vaccines. Just 10% of agency employees work in the Washington, D.C., area.

“Much of our workforce lives in rural areas, so the vaccine hesitancy that has been documented in rural America very much applies to our employees,” said a USDA official who spoke on the condition of anonymity because of the sensitivity of the issue.

Some waiver requests have been approved, said the official, who did not offer details or say how the agency plans to deal with them.

The prospect of working side by side with unvaccinated colleagues is unsettling to many staffs that are already doing it.

“Everybody is masked, but there is no way to stand six feet apart in a processing plant,” said Paula Schelling-Soldner, chairwoman of the National Joint Council of Food Inspection Locals, which represents about 6,400 meat and poultry inspectors, a group that has worked through the pandemic. She said 600 to 700 of the workforce of 10,000 inspectors have applied for religious or medical exemptions.

VA, with about 40,000 holdouts, requires weekly testing for employees on medical staffs, a workaround that makes some colleagues uneasy.

“You could be tested on a Monday and get the virus on Tuesday and still be at work the rest of the week,” said Kelli Michels, a nurse and executive vice president of Local 3669 of the American Federation of Government Employees. The local represents the staff of the Minneapolis VA Health Care System, which has faced hundreds of absences because of omicron in recent weeks.

The Office of Personnel Management has urged agencies to start testing unvaccinated employees at least weekly by Feb. 15, either in the office, at outside locations or through self-administered tests that are verified. Standing up such a system and potentially signing new contracts with outside providers poses a big challenge; a similar request to set up a testing system failed last summer. At the time, senior managers worried how to protect their staffs’ vaccination status, track testing results and quickly negotiate contracts, officials said.

“Do people have to get tested every day? Twice a week?” asked Jason Briefel, a partner at Shaw Bransford & Roth and executive director of the Senior Executives Association, which represents senior leaders in the government. “The testing situation last year clearly didn’t work. Setting these things up isn’t easy.”

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