WASHINGTON — Thousands of IRS employees will be furloughed as the partial government shutdown drags on, the tax-collecting agency notified employees on Wednesday. 

The updated IRS Lapsed Appropriations Contingency Plan calls for 39,870 IRS employees, or 53.6% of staff, to be retained as the shutdown enters its second week. 

Those who work through the shutdown will be paid with “non-expiring funds.”

 Of the nearly 40,000 staffers being kept on, 24,470, work in the IRS’s Taxpayer Services division.  

The agency’s initial contingency plan called for all employees to remain on the job for at least the first five business days of the shutdown, but did not specify what would happen should the funding lapse last beyond Oct. 7.

The furloughs are being implemented a week before the Oct. 15 deadline to file 2024 federal tax returns for Americans who were granted an extension.

The National Treasury Employees Union, a labor group that represents tens of thousands of IRS employees, said the public should expect processing delays because of the furloughs.   

“Due to the government shutdown the American people lost access to many vital services provided by the IRS when the agency furloughed thousands of employees,” National Treasury Employees Union (NTEU) said in a statement. “Expect increased wait times, backlogs and delays implementing tax law changes as the shutdown continues.” 

“Taxpayers around the country will now have a much harder time getting the assistance they need, just as they get ready to file their extension returns due next week.”

The group criticized the “complete lack of planning” from the IRS that left tens of thousands of employees “in the dark about their work status until their supervisor informed them today.”

“Every day these employees are locked out of work is another day of frustration for taxpayers and a growing backlog of work that sits and waits for the shutdown to end,” the union said. 

NTEU urged congressional lawmakers and the Trump administration to reach an agreement that reopens the government.  

Furloughed IRS workers, as well as those still on the job without compensation, were notified by the agency that they would receive backpay at the conclusion of the shutdown, according to the Associated Press. 

President Trump suggested last week that some of the 750,000 federal workers estimated to be furloughed each day during the shutdown could potentially be fired by his administration.

All but three Senate Democrats have repeatedly refused to vote for a Republican-backed short-term spending bill that would keep the government funded at pre-shutdown levels until Nov. 21. 

Democrats want an extension of pandemic-era ObamaCare subsidies and a rollback of changes to Medicaid payment and eligibility rules included in any continuing resolution that would reopen the government.