The order came hours before Thursday’s 23:59 ET (04:59 GMT Friday) deadline for federal workers to accept the deal.
A lawyer for the justice department said the White House’s Office of Personnel Management would notify federal employees that the deadline had been paused, CBS reported.
The White House, in a statement, appeared to see the temporary halt as a way to increase the number of resignations by extending the deadline.
“We are grateful to the Judge for extending the deadline so more federal workers who refuse to show up to the office can take the Administration up on this very generous, once-in-a-lifetime offer,” press secretary Karoline Leavitt said in a statement.
An OPM official said that the agency would continue processing resignations until the Monday hearing.
The Trump administration, which previously said it hoped for as many as 200,000 people to accept its offer, told US media they expected a spike in participation just ahead of the deadline.
“We expect the number to increase,” Leavitt told reporters outside the West Wing before the judge paused the programme. “It’s going to save the American people tens of millions of dollars.”
Leavitt added that the administration encourages workers to “accept the very generous offer”.
“If they don’t want to show up to the office, if they want to rip the American people off, then they’re welcome to take this buyout, and we’ll find highly competent individuals who want to fill these roles,” she said.
An analysis of the federal workforce by the non-profit Partnership for Public Service found that the annual attrition rate among federal employees is normally about 6%.
The American Federation of Government Employees, a union, filed the lawsuit against the White House Office of Personnel Management, arguing it had violated the law, that it could not fund the deal, and that it had given conflicting guidance about its terms.
AFGE had previously warned its members “NOT to resign or respond” to the White House’s resignation package.
The union had said in an email to members that the offer was part of an “effort to dismantle the civil service and replace the skilled, professional workforce with unqualified political appointees and for-profit contractors”.
The union noted that Congress has not passed a budget for funding beyond mid-March, arguing that it was unclear whether agencies could pay workers until September.
“There is not yet any evidence the administration can or will uphold its end of the bargain, that Congress will go along with this unilateral massive restructuring, or that appropriated funds can be used this way, among other issues that have been raised,” AFGE said.
Some federal employees had said that the buyout proposal – delivered in the form of a late-night email with the subject line “Fork in the Road” – came as a shock. They said they worried about unanswered questions with the process and its legality, which has piled on uncertainty to an already hectic start to Trump’s second term.
“The tone of the initial email was like ‘you may be cut anyway,’” Monet Hepp, a medical support specialist at the US Department of Veterans Affairs, previously told BBC. “People were blindsided by it.”
Some employees thought the email was spam, as it was such a departure from typical government communications, causing them initially to delete it.
“I want to confirm that this is a legitimate communication from OPM,” a public affairs officer with the Department of Veterans Affairs, wrote in an email that was sent to employees and shared with the BBC.
Democrats have questioned the legality of the resignation package and warned it would lead to a “brain drain” that would be “felt by every American”.
“Without the expertise and institutional knowledge that so many federal employees bring to their work, our government will be incapable of responding effectively to national emergencies, serving the American public, or even carrying out routine operations,” Democrats on the House Oversight Committee wrote in a letter to President Trump.
On Tuesday, the Central Intelligence Agency (CIA) became the first national security department to extend the offer to its staff, telling its entire workforce they could quit and receive about eight months of pay and benefits.
Former US intelligence officials and several lawmakers have raised concerns that this offer could undermine US national security priorities.
Senator Mark Warner of Virginia, the vice-chairman of the Senate Intelligence Committee, cautioned CIA employees against taking the offer.
“There are few government agencies more essential to our national security than the CIA,” Warner said in a statement.
“A lot of federal employees, including at the CIA, are my constituents, and I’ve been warning them that these ‘buyouts’ are empty promises, since Congress hasn’t approved any money to do it.”
There are also reports that the Trump administration’s Department of Government Efficiency (Doge) is targeting the National Oceanic and Atmospheric Administration.
The US government agency is tasked with weather forecasting, monitoring conditions in the ocean and atmosphere and managing fishing and protections for endangered marine life.
It runs several agencies, including the National Weather Center – which has forecasting offices in cities and states across the US and helps predict everything from tornadoes to hurricanes.
Those who work for Doge, which is led by billionaire Elon Musk, have been inside the NOAA offices and employees have been told to expect that its budget and half the workforce will be cut, sources told CBS.
Sen Chris Van Hollen, who represents Maryland – where NOAA is headquartered, said his office was investigating the reported cuts.
“NOAA is vital for weather forecasting, scientific research & more,” he said. “Their critical work saves lives.”
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