The Internal Revenue Service had barely begun bringing its lowest-paid workers back to the office in late April when someone in the Philadelphia call center came down with a fever, forcing the third-floor staff to head home.

Within two days, an employee in the processing center in Kansas City, Mo., who routes paper checks for deposit was sick with symptoms of the novel coronavirus, too. Then the husband of a woman in accounts management in the Covington, Ky., office tested positive, leading managers to presume that she was infected.

The three service centers, among 10 campuses nationwide where the IRS is trying to reinstate 11,000 employees, had to partially close for a week for deep cleaning.

The infections were just the first hurdle for an agency desperate to reconnect with tens of millions of taxpayers it has struggled to serve since late March.

The tax behemoth that touches virtually every American has made the government’s most aggressive effort so far to recall its workforce. But like other federal agencies following President Trump’s order to reopen the country, the IRS is struggling to ensure the safety of its employees as it tries to chip away at a crushing backlog and serve the public.

The staffing shortage will prolong delays — refunds for paper tax filers, responses to amended tax returns, returns frozen after they were flagged for identity theft. The Austin office is backed up with 250,000 paper-heavy requests for taxpayer identification numbers from foreign-born taxpayers who are not eligible for Social Security numbers.

No federal leaders could fully prepare for a disruption on this scale. Yet the IRS, awash in sensitive taxpayer information, finds itself in a morass brought on by years of crippling budget cuts, cumbersome paper-based systems and resistance to telework.

The challenges seem insurmountable. Even before the recent coronavirus infections, few employees felt secure enough to go back. As of Monday, about 3,000 customer-service and clerical workers had volunteered to return to the office, an absentee rate of almost 75 percent.

The agency central to implementing the Treasury Department’s $2.1 trillion economic relief package has offered only recorded messages to millions of taxpayers wanting to ask a human when their refunds and stimulus checks will arrive — although it is slowly opening toll-free phone lines, including for tax preparers, businesses and those with questions about stimulus checks. Callers can expect long waits.

The IRS has extended the April 15 filing deadline to July 15 for the first time since the date was fixed in 1955. Still, a workforce that sorts mail by hand and conducts some business by fax has been left in the thick of tax season with millions of pieces of untouched correspondence piled into 53-foot trailers at nearby postal processing centers. Managers in Florence, Ky., had to lease new office space to hold their mail, installing doors and security cameras to ensure the safety of taxpayer information.

“I don’t think I can think of a word to overstate the negative impact on our mission,” said Chad Hooper, a quality-review manager who is national president of the IRS’s Professional Managers Association. “The backlog of work is incredible.”

The agency managed in three weeks to push out 80 million of 150 million electronic stimulus payments, showing its agility even with software programming language that dates to the Kennedy administration. Electronic tax returns are being processed quickly, but millions of refunds for paper returns will be delayed by months.

“It’ll be an understatement if I were to call this a unique situation,” Sunita Lough, the agency’s deputy commissioner for services and enforcement, said in a recent interview.

“We understand the financial needs of taxpayers and the liquidity and money they need,” Lough said. “But we’ve had to take extraordinary steps to alleviate those concerns and balance the health and safety of our employees.”

The agency, in a shift, is now requiring workers to return. Commissioner Charles Rettig told his workforce in an email Tuesday that employees in Texas, Utah and Kentucky who can’t telework must report to their offices June 1 to handle the extended filing season. Staff members will be called back in reverse order of seniority, with exceptions for those with existing health conditions.

Other federal agencies are mapping out return-to-the-office strategies, weighing staggered shifts, sustained telework, child-care schedules, public transportation options and shelter-in-place orders.

They have only vague guidance from the top. The Office of Personnel Management early this month told agencies to begin “a phased transition to normal operations” in line with national guidelines to “open up America again.” They were instructed to take into account state and local restrictions “and other factors.”

The coronavirus restart, like the shutdown, is unfolding unevenly. Some national parks have reopened. The Federal Trade Commission is working from home through June, and the military has restricted troop movements until then. The Department of Housing and Urban Development is letting each supervisor determine whom to bring back to the office.

“There’s been no clear, consistent guidance and leadership from the top,” said Gerald E. Connolly (D-Va.), chairman of the House subcommittee that oversees federal agencies. He described “a lot of confusion and contradictory guidance” that has unnerved much of the workforce, including at the IRS.

On the front lines

To coax their $15-an-hour staffers back, managers offered temporary bonus pay and telework when things get back to normal, a boon to employees who have never had the luxury of working from home.

In the meantime, those on the front lines of a new, untested pandemic office culture fear for their safety — masks, gloves and hand-washing breaks notwithstanding.

“IRS employees are very proud of our work,” said Debbie Mullikin, president of Local 73 of the National Treasury Employees Union (NTEU), which represents 2,200 employees in Cincinnati, Covington and Florence. “It’s a source of stress knowing we’re going to come back to a huge pile of work at the apex of refund season.”

“We’re worried,” Mullikin said. “The IRS doesn’t do contact tracing. No one was made aware who came into contact with the individual who was sick.”

The returning employees were told to bring their own masks, until a vendor in Upstate New York came through at the last minute with 1 million three-ply surgical masks that were shipped around the country. Reusable cloth masks are on order.

Since the presumptive positive case, Mullikin said her email inbox and Facebook page have blown up with questions from anxious colleagues.

More than half the IRS’s staff of 76,340 is over 50, making it among the oldest workforces in the government, federal data shows, and thus more vulnerable to the coronavirus.

An estimated 101 federal employees have died of covid-19, the disease caused by the virus, and nearly 14,300 have tested positive for the virus, according to the watchdog group Accountable.US. Among them are 195 IRS workers who have been infected, with four deaths.

Telework has kept many federal offices afloat during the pandemic. But for much of the IRS, it wasn’t an option. From the moment Rettig shut down a majority of agency operations on March 30, it was clear that services to taxpayers would suffer in unprecedented ways.

The agency was still implementing the last of 119 provisions of the tax law Congress passed in 2017. Tax season was peaking. But just under half of the IRS workforce wasn’t set up to work from home, leaving the mailrooms, call centers, tax return processing centers and walk-in help centers empty. The employees went on paid leave.

The rest began logging in from home on laptops that, before the pandemic, they used a few days a month. For some, it was a bumpy transition, as many of these employees deal with sensitive information they can’t access from home. Others couldn’t retrieve documents left behind at the office.

One manager had to wait weeks for permission to have staffers order stamps online from the U.S. Postal Service so they could correspond directly with taxpayers appealing enforcement actions.

Soon after extending the filing deadline, agency leaders suspended a slew of tax enforcement efforts and halted new audits and collections until July.

They got creative, turning to fax machines instead of paper forms to implement key provisions of the economic stimulus legislation for businesses. In a break with tradition, rules on original signatures were relaxed to make way for electronic signatures via DocuSign. And leaders started sending new laptops through the mail to homebound employees.

White House economic adviser Kevin Hassett said on May 10 that Americans face an economy that will worsen in the coming months. (Reuters)

But there have been limits.

Paper transactions are still a backbone of IRS operations. Mail must be opened and scanned. Returns must be sorted, coded, edited and numbered. Return data must be entered into computers. Valid transactions must be posted to a master file that dates to the early 1960s. Refunds or balance-due notices must be issued to taxpayers. Paper returns must be retired to federal record centers.

All of this is manual work. Most of it isn’t getting done.

Outdated technology

The IRS has the oldest technology systems in the federal government, and with more than half its staff now at home, videoconferencing and virtual meetings are off-limits to preserve server bandwidth. Some employees in Philadelphia, Kansas City and Memphis have been unable to telework because they would crash the system’s antiquated servers, said Hooper, the quality-review manager.

The agency, in its haste to get payments out, was unable to keep up with unexpected mishaps that quickly overwhelmed the system in April once the government started issuing stimulus checks.

Some taxpayers didn’t receive payments for their dependent children. Several million filers who used tax preparers didn’t get their checks at first because the IRS didn’t have their direct-deposit information. Checks went to dead taxpayers. Then the pages the agency set up on its website to help people track the status of their payments were unresponsive for weeks.

Robert Caarni, 54, says he’s still waiting for his $1,200 stimulus check. He lives on disability — $12,826 a year — in Williamsburg, Va., because of severe depression and is staying free at a motel after losing his home a few months ago.

He’s been obsessively dialing the toll-free phone line during business hours only to hear a recorded message telling him that the IRS is closed and directing him to the website, where his payment status has been unavailable. “I’ve been calling every day since April,” he said, “and I can’t get to a real person.”

Many of these problems have eased. But the IRS still isn’t answering most of the calls it receives.

Even before the pandemic, the agency struggled to provide responsive customer service as Republicans in Congress repeatedly cut its budget and its overall staffing levels fell by 20 percent since 2008.

“This is what happens when you take an agency as important as the IRS and you start to drown it with budget cuts,” said Tony Reardon, the NTEU national president.

In normal circumstances, the IRS handles 100 million phone calls a year. It has no way of knowing how many people have tried to reach a live person in the past seven weeks. Twenty-three percent of callers spoke to a live assister during the 2019 filing season, according to a report by the Taxpayer Advocate Service. The agency’s budget that year was its lowest in 20 years, after adjusting for inflation.

Under pressure from the union, the agency agreed three years ago to implement a pilot program to let phone assisters work from home. It was largely successful, union and management officials said. But just a tiny fraction of the 16,000 assisters were permitted to answer phones at home, even though their laptops take calls through voice recognition software.

The IRS’s Lough said that while telework “is a great way for people to work from home, it always has its pros and cons.”

“It’s not as simple as having a laptop to take voice-over-IP calls,” she said. “Lines must be secure. We have to have the right infrastructure.”

Taxpayers have been unable to communicate with the IRS online. Its interactive services are limited to checking on the status of a refund or an amended return — but only after a taxpayer has filed a return. The system doesn’t allow questions in real time, largely because of outdated technology and privacy concerns.

The small number of employees now back at the office are adjusting to a new workplace. There are hourly breaks for hand-washing. Every other cubicle is empty for social distancing. Everyone has to bring lunch, because the canteens are closed. Employees who show up at least four days a week for 20 days get a $500 bonus.

The IRS normally would be preparing this month for next year’s tax season, writing guidance and new computer codes to implement tax code changes ordered every year by Congress. It’s a lumbering process slowed by old technology, requiring 60 different tax processing systems to be reformatted across the agency’s business units.

“I would have thrown myself across the railroad tracks if I were still there,” said Terry Milholland, a former chief information and technology officer who retired in 2016, “and said, ‘This is crazy. I’m not sure we can do this.’ ”