WASHINGTON — The Trump administration on Tuesday took another significant step to discourage migrants from seeking asylum, issuing an order that could keep thousands of them in jail indefinitely while they wait for a resolution of their asylum requests.

The order issued by Attorney General William P. Barr was an effort to deliver on President Trump’s promise to end the “catch and release” of migrants crossing the border in hopes of escaping persecution in their home countries.

The order — which directs immigration judges to deny some migrants a chance to post bail — will not go into effect for 90 days. It is all but certain to be challenged in federal court, but immigrant rights lawyers said it could undermine the basic rights of people seeking safety in the United States.

“They want to send a message that you will get detained,” said Judy Rabinovitz, a deputy director of the Immigrants Rights’ Project at the American Civil Liberties Union. “We are talking about people who are fleeing for their lives, seeking safety. And our response is just lock them up.”