WASHINGTON — A sharply divided Supreme Court on Wednesday reinstated a lower-court order for the Trump administration to release frozen foreign aid, but it was not clear how quickly money would start flowing.

By a 5-4 vote, the court rejected an emergency appeal from the Republican administration, while also telling U.S. District Judge Amir Ali to clarify his earlier order that required the quick release of nearly $2 billion in aid for work that had already been done.

Although the outcome is a short-term loss for President Donald Trump’s administration, the nonprofit groups and businesses that sued are still waiting for the money they say they are owed. Organizations in the U.S. and around the world have cut services and laid off thousands of workers as a result.

HIAS, one of the nonprofit groups in the case, said it was encouraged to see the Trump administration held accountable, but said it regretted “the irreparable damage that the Trump administration has already inflicted on our staff, the people we serve, and the reputation of the United States as a leader and a reliable partner.”

The Maryland-based group has worked on refugee issues for more than a century, including giving potential refugees support to stay in their home countries.

Justice Samuel Alito led four conservative justices in dissent, saying Ali lacks the authority to order the payments. Alito wrote that he is stunned the court is rewarding “an act of judicial hubris and imposes a $2 billion penalty on American taxpayers.”