The IRS will exempt more than half of its total workforce if the partial government shutdown extends into the upcoming filing season, according to updated guidance the agency released Tuesday.

A vast majority of the agency’s staff have been furloughed since the beginning of the shutdown on Dec. 22, but the IRS plans to call back 46,000 employees, or 57 percent of its workforce, to help issue refunds for the tax season that opens on Jan. 28. Most would continue to work without pay while the shutdown continues.

The updated guidance exempts federal employees “necessary for the payment of refunds,” a reversal from the decision the Office of Management and Budget made in 2011, when it directed the IRS not to pay refunds when a shutdown appeared likely, but was averted.

Despite a lapse in appropriations, the IRS can still issue tax refunds and because they’re paid from a “permanent, indefinite refund appropriation” that also covers “activities necessary to issue the refunds,” the guidance states.

The updated guidance doesn’t exempt employees for audit functions or examination of tax returns. “Planning, research, and training and development activities” would also remain non-essential during the filing season.

A federal judge on Tuesday denied the National Treasury Employees Union’s request for an immediate temporary restraining order that would stop the Trump administration from spending money not yet appropriated by Congress.

“There is no doubt the IRS needs to get ready for the 2019 filing season that starts Jan. 28, and IRS employees want to work. But the hard, cold reality is that they’ve already missed a paycheck and soon they’ll be asked to work for free for as long as the shutdown lasts,” NTEU president President Tony Reardon said in an email.

The next hearing in the case for a preliminary injunction is scheduled for Jan. 31.

“While we are disappointed that the judge did not take immediate action, we look forward to continuing our argument that the administration cannot require more and more employees to report to work without pay,” Reardon said.

The guidance notes that the chief information officer is on-track to update all the IT systems and forms needed in time for the upcoming filing season.

Since the beginning of the shutdown, the IRS has exempted 10,000 IRS employees or about 12.5 percent of its workforce. A significant number of those employees work in the agency’s  IT and criminal investigations division.

Under a fiscal 2018 filing season contingency plan, the agency planned to exempt 43.5 percent of its total workforce.

If Congress and President Donald Trump don’t reach a deal to fund shuttered agencies soon, Reardon expressed concerns that “highly trained IRS employees will consider quitting” in order to get paid.

An IRS spokesman on Tuesday said the agency is “starting the process to recall these employees in the coming days.”

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