The case raises questions about the Trump administration's adherence to limits set by the Supreme Court. It carries the risk of a significant clash between the two coequal branches of government and potentially a full-blown constitutional crisis.

Justices Clarence Thomas and Samuel A. Alito Jr. dissented. A group of migrants had been scheduled to be flown out of the country, according to people familiar with the matter.

In a brief order, the court directed the Trump administration not to remove Venezuelans held in Northern Texas “until further order of this court.”