Demonstrator hold signs during a protest rally by government workers and concerned citizens against the government shutdown on Friday, January 11, 2019 at Post Office Square near the Federal building, headquarters for the EPA and IRS in Boston.

Thousands of recalled employees at the IRS missed work this week, despite being summoned back to work amid the partial federal shutdown.

As many as 14,000 staffers at the tax agency did not come into the office, CNBC has confirmed.

A number of employees have received permission from their managers to miss work, citing financial hardship.

News of the absences arrives a week after the IRS released its contingency plan for the tax filing season, which begins on Monday, Jan. 28. The agency called for more than half of its staff — roughly 46,000 people — to return to work.

President Donald Trump and lawmakers on Friday reached a deal to fund the government for at least three weeks, ending the longest government funding lapse on record.

"After a month with no pay, real hardship does exist for IRS employees, including not having the money needed to get back and forth to work or to pay for the child care necessary to return to work right now," said Tony Reardon, president of the National Treasury Employees Union.

"The longer employees go without pay, more face financial hardships," he said.

The IRS did not immediately return calls for comment.

Given the shutdown, expect to experience hiccups as you prepare to submit your tax return.

For instance, live customer service via phone isn't available, but the IRS has said it will add workers to cover the lines. You can expect lengthier wait times if you're calling with questions.

Further, taxpayer assistance centers are closed during the shutdown. That means you won't be able to get any help in person.

Here's what else you should know.