As a result, millions of individual taxpayers and businesses could face lengthy delays before they receive refunds they desperately need as the coronavirus halts their incomes. Taxpayers disputing how much they owe or waiting to see if they qualify for tax credits also could have to wait indefinitely.

“Clearly, most day-to-day operations at the IRS have stood down, that’s the blunt reality,” said a former commissioner, Mark Everson, who ran the agency from 2003 until 2007.

The delays in handling paper correspondence are coming as the agency grapples with getting the stimulus payments out. The process kicked off this week with direct deposits to tens of millions of Americans, and almost immediately hit some bumps.

Many taxpayers took to Twitter to vent about not being able to navigate or access an online IRS payment tracking tool, or having their payments misrouted to their tax preparers. Spokespeople for two of the biggest tax software companies, TurboTax-maker Intuit and H&R Block, said their systems weren’t at fault.

“We share our clients’ frustration that many of them have not yet received these much-needed payments due to IRS decisions, and we are actively working with the IRS to get stimulus payments sent directly to client accounts,” H&R Block’s spokesperson said.

The IRS will face another big test next week, when paper checks for the stimulus payments are supposed to start going out to people who don’t have direct deposit information on file with the agency.

Meanwhile, tax returns for the 2019 tax year, along with refunds, are still being processed, at least the ones that are filed electronically, as the vast majority are these days. But many other, more routine things are falling through the cracks, tax preparers and others who deal with the agency say.

It’s an unprecedented challenge for a federal agency that arguably affects more Americans than any other, exacerbated by a decade of budget cuts by Congress and a workforce that has shrunk by roughly 22 percent since 2011.

The myriad closures will inevitably inconvenience taxpayers and professionals who represent them, said another former commissioner, John Koskinen. But he added that agency managers have an obligation to give employees a safe working environment.

Still, Koskinen didn’t play down some of the consequences, such as the halt in processing paper returns. Even though only about 10 percent of individual taxpayers mail returns instead of electronically filing them, that amounts to 15 to 16 million people, many of whom will have to wait for refunds just as they, and the economy, need them most.