Roberts offered no rationale for his decision. He issued it around 9:30 p.m. on Wednesday in a form that the justices typically use to pause lower-court proceedings temporarily while the high court considers how to proceed. The chief justice ordered the aid groups that filed the lawsuits to respond to the government’s application by noon on Friday.

Roberts is virtually certain to refer the matter to the full Supreme Court, and his stay is likely to remain in place until the full court acts.

Ali, an appointee of former President Joe Biden, ordered the administration on Tuesday to pay the accumulated bills by the end of the day on Wednesday. The judge acted after finding that the Trump administration had essentially flouted earlier orders he issued requiring the State Department to lift a blanket freeze on overseas aid programs.

Rather than take steps to unfreeze that aid, as Ali had directed Feb. 13, the State Department and the U.S. Agency for International Development found new legal rationales to keep it on hold, the judge said.

As a result, Ali gave the administration the midnight Wednesday deadline to send the payments for what officials have estimated is $2 billion-worth of unpaid work completed by aid contractors.

Groups and businesses that administer programs funded by U.S. foreign aid say the abrupt freeze — which resulted from President Donald Trump’s Day 1 executive order calling for a “pause” on all foreign assistance — has devastated thousands of organizations and resulted in closures, layoffs and the end of life-saving humanitarian work around the world. And they say that the Trump administration’s efforts to terminate contracts and shut off the flow of aid have continued unabated since Ali issued orders to lift the spending freeze.

The Trump administration disclosed Wednesday that it is eliminating more than 90% of USAID foreign-aid contracts — and cutting $60 billion in foreign assistance overall.

Peter Marocco, the Trump appointee leading USAID’s day-to-day operations, filed a statement with Ali Tuesday suggesting that it would be impossible to meet his quick deadline and in fact would require “weeks’ of work to restart dismantled payment systems.

“Restarting funding related to terminated or suspended agreements is not as simple as turning on a switch or faucet,” Marocco said. “Rather, the payment systems of USAID and State are complicated and require various steps before payments are authorized to be disbursed by the U.S. Treasury, Department of Health and Human Services, and/or the Department of State, involving multiple agencies.”

But the foreign-aid groups argue that the government’s problems meeting the judge’s midnight deadline were a result of its own decisions. The administration, the groups say, should never have shut down functional payment systems without a ready replacement and should not have circumvented Ali’s initial order to restart them in the first place. They also said there were significant safeguards in place to ensure outgoing funds were for legitimate bills.

Harris filed the emergency petition with the justices at roughly the same time that a federal appeals court in Washington denied a similar emergency appeal of Ali’s decision. The unanimous three-judge appellate panel noted that temporary restraining orders of the kind Ali issued typically cannot be appealed, and there was no reason to depart from that practice in this case. The ruling left the Supreme Court as the last resort for the Trump administration.

Harris said the administration was prepared to pay any bills for completed work but suggested that the need to conduct a review for waste, fraud and abuse required a lengthier process than the one permitted by Ali’s orders.

“To be very clear, the government is committed to paying legitimate claims for work that was properly completed pursuant to intact obligations and supported by proper documentation,” Harris wrote. “It is attempting to navigate the district court’s evolving orders — and the ensuing, resource-consuming contract-review process — as best it can.”

Harris also contended Ali had no authority to intervene in the matter in the first place, suggesting he was impinging on Trump’s authority to direct the nation’s foreign policy.

“The President’s power is at its apex and the power of the judiciary is at its nadir in matters of foreign affairs,” Harris wrote.

The effort by the Trump administration to quickly dismantle USAID and curtail its international grants and contracts has become one of the most intense legal fights of Trump’s second term. Another federal judge, Trump appointee Carl Nichols, briefly blocked Trump appointees’ efforts to put thousands of USAID workers on administrative leave, including hundreds stationed overseas. But Nichols lifted his blockade last week.

Other groups that rely on foreign-aid funds have also sued, including personal service contractors and the U.S. Conference of Catholic Bishops.