A divided US Supreme Court declined on Wednesday to let President Donald Trump’s administration withhold payment to foreign aid organisations for work they already performed for the government as the Republican president moves to pull the plug on American humanitarian projects around the world.

Handing a setback to Trump, the court, in a 5-4 decision, upheld Washington-based US District Judge Amir Ali’s order that had called on the administration to promptly release funding to contractors and recipients of grants from the US Agency for International Development (USAID) and the State Department for their past work.

Chief Justice John Roberts and fellow conservative Amy Coney Barrett joined the court’s three liberal members to form a majority in rejecting the Trump administration’s request. Conservative Justices Samuel Alito, Clarence Thomas, Neil Gorsuch and Brett Kavanaugh dissented from the decision.

The order by Ali, who is presiding over an ongoing legal challenge to Trump’s policy, had originally given the administration until February 26 to disburse the funding, which it has said totalled nearly $2 billion that could take weeks to pay in full.

Roberts paused that order hours before the midnight deadline to give the Supreme Court additional time to consider the administration’s more formal request to block Ali’s ruling. The Supreme Court’s 6-3 conservative majority includes three justices Trump appointed during his first presidential term.

The court did not provide a rationale for its unsigned order. With the original deadline now lapsed, the court instructed Ali to “clarify what obligations the government must fulfil to ensure compliance with the temporary restraining order, with due regard for the feasibility of any compliance timelines”.

Ali has a hearing scheduled for Thursday at the request of the plaintiffs for a preliminary injunction. The judge has a temporary restraining order currently in place that lasts through March 10.

Alito, in a dissent joined by three fellow conservatives, expressed dismay at the court’s decision.

“Does a single district court judge who likely lacks jurisdiction have the unchecked power to compel the government of the United States to pay out (and probably lose forever) 2bn taxpayer dollars? The answer to that question should be an emphatic ‘No,’ but a majority of this court apparently thinks otherwise,” Alito wrote. “I am stunned.”

The Republican president, pursuing what he has called an “America First” agenda, ordered a 90-day pause on all foreign aid on his first day back in office on January 20.

That order and ensuing stop-work orders halting USAID operations around the world have jeopardised the delivery of life-saving food and medical aid, throwing global humanitarian relief efforts into chaos.

Aid organisations sued Trump for exceeding his authority under federal law and the US constitution by effectively dismantling an independent federal agency and cancelling spending authorised by Congress.

Among the plaintiffs in the litigation are the AIDS Vaccine Advocacy Coalition, Journalism Development Network, international development company DAI Global and refugee assistance organisation HIAS.

Acting Solicitor General Sarah Harris said in a Supreme Court filing on March 3 that blocking Ali’s order was “warranted to prevent reinstatement of a new, short-fused deadline that would unlawfully commandeer federal payment processes anew”.

Harris argued that the judge’s order amounted to judicial overreach and had given the administration too little time to scrutinise the invoices “to ensure the legitimacy of all payments”.

Lawyers representing the administration said in a separate February 26 filing that full payments could take weeks.

‘Extraordinary and irreversible’

Aid organisations said in a Supreme Court filing on February 28 that they “would face extraordinary and irreversible harm if the funding freeze continues”, as would their employees and those who depend on their work.

The work done by the organisations “advances US interests abroad and improves — and, in many cases, literally saves — the lives of millions of people across the globe. In doing so, it helps stop problems like disease and instability overseas before they reach our shores”, lawyers for the foreign aid groups wrote.

“The government’s actions have largely brought this work to a halt,” the lawyers wrote, adding that the Trump administration “comes to this court with an emergency of its own making”.

The Trump administration had kept the disputed payments largely frozen despite a temporary restraining order from Ali that they be released and multiple subsequent orders that the administration comply.

Ali’s February 25 enforcement order at issue before the Supreme Court applied to payment for work done by foreign aid groups before February 13, when the judge issued his temporary restraining order.

Ali, who was appointed by Democratic former president Joe Biden, issued his temporary restraining order to prevent irreparable harm to the plaintiffs while he considered their claims.

Trump and his adviser, Elon Musk, the world’s wealthiest person, have taken dramatic steps to reshape and shrink the federal government. They have dismantled some agencies, fired thousands of workers, dismissed or reassigned hundreds of officials and removed the heads of independent agencies, among other actions.

As he moves to end American-backed humanitarian efforts in numerous countries, Trump’s administration has sent funding termination notices to key organisations in the global aid community.

Global aid groups have said the US retreat endangers the lives of millions of the world’s most vulnerable people, including those facing deadly diseases and those living in conflict zones.