A federal judge in Boston said on Tuesday that the Trump administration had apparently violated an order he issued in April by flying a Burmese immigrant to South Sudan without first giving him enough time to challenge his removal over fears about being sent to a country not his own.

The stern remarks by the judge, Brian E. Murphy, came at a hearing in Federal District Court in Boston where immigration lawyers raised concerns that at least one other immigrant had also been flown to South Sudan without proper due process.

“I can tell you it sounds like this deportation would be a violation of my preliminary injunction,” Judge Murphy said.

During the hearing, Judge Murphy ordered a lawyer for the Justice Department, Elianis N. Perez, to notify everyone involved in the flight to South Sudan — from the pilot of the plane to officials at the Department of Homeland Security — that they could face criminal contempt sanctions if his ruling was not followed. He also instructed Ms. Perez to find out exactly where the plane was and whether it could be turned around midflight.

“Where is the plane now?” Judge Murphy asked at one point.

“I do not know,” Ms. Perez said.

It was not clear how many, if any, other migrants were on the plane or what their home countries were.

The contentious courtroom back-and-forth emerged from a ruling that Judge Murphy issued in April, directing the Trump administration not to deport immigrants to countries other than their own without first giving them 15 days’ notice to raise concerns that they might face danger there.