A federal judge on Tuesday ordered the Trump administration to not let a group of migrants being flown to South Sudan leave the custody of US immigration authorities after saying they appeared to have been deported in violation of a court order.

US District Judge Brian Murphy in Boston during a hastily arranged virtual hearing said that while he was not going to order the airplane to turn around, that was an option the US Department of Homeland Security could employ to comply with his order.

Murphy warned that officials could be held in criminal contempt if he found they violated his previous order barring the swift deportation of migrants to countries other than their own before they could raise any concerns that they might face torture or persecution there.

"I have a strong indication that my preliminary injunction order has been violated," Murphy told Elianis Perez, a lawyer with the US Department of Justice.

Murphy, an appointee of former Democratic President Joe Biden, said any migrants covered by the injunction en route to the African nation must remain in the government's custody pending a further hearing on Wednesday.

He said the Department of Homeland Security, which oversees US Immigration and Customs Enforcement, could comply with that order in a myriad of ways, including keeping the migrants on the plane on the tarmac once it lands.

"I'm not going to limit DHS on where they hold them," Murphy said. "If they want to turn the plane around, they can."

The agency did not respond to requests for comment.

The development marked a new clash between the federal judiciary and Republican President Donald Trump's administration in its efforts to implement Trump's calls for mass deportations as part of his hardline immigration agenda.

Another jurist, US District Judge James Boasberg in Washington, last month found "probable cause" to hold officials in criminal contempt for violating his order halting deportations of alleged members of a Venezuelan gang who had no chance to challenge their removals.

The US Supreme Court on Friday maintained a block on Trump's deportations of Venezuelan migrants under a 1798 law historically used only in wartime, faulting his administration for seeking to remove them without adequate due process.

'PLEASE HELP!'

The class action lawsuit before Murphy was filed after the Department of Homeland Security in February instructed immigration officers to review cases of people granted protections against being removed to their home countries to see if they could be re-detained and sent to a third country.

Murphy issued a preliminary injunction on April 18 designed to ensure any migrants being sent a third country were provided due process under the US Constitution's Fifth Amendment and a "meaningful opportunity" to raise any fears for their safety.

In a motion filed earlier Tuesday, a lawyer for the plaintiffs said they learned that nearly a dozen migrants held at a detention facility in Texas were being flown to South Sudan, whose conditions have long been dangerous even for locals.

The United Nations has warned that the country's spiralling political crisis could reignite the brutal civil war that ended in 2018.

Among the migrants on the plane was a Vietnamese man who was being held at the Port Isabel Detention Center in Texas. Perez during Tuesday's hearing said the man had been convicted of murder, and a top lawyer with the Department of Homeland Security said the plane had at least one rapist on it, too.

The Vietnamese man's spouse had emailed his lawyer saying that he and 10 other individuals were believed to have been deported to South Sudan. The group also included nationals of Laos, Thailand, Pakistan and Mexico, the spouse said.

"Please help!" the spouse wrote. "They cannot be allowed to do this."

Lawyers for the migrants said an attorney for another individual from Myanmar likewise had been notified he was being sent to South Sudan.

Yet Perez later Tuesday said the man was instead flown to Myanmar. She could not explain the change in destination, which a lawyer for the migrants, Trina Realmuto of the National Immigration Litigation Alliance, said "defies logic."

Murphy has previously modified his injunction to guard against the possibility of DHS ceding control of migrants to other agencies to carry out rapid deportations, after the Trump administration took the position that the US Department of Defense was not covered by Murphy's orders.

The administration made that argument after acknowledging the Defense Department flew four Venezuelans held at Guantanamo Bay in Cuba to El Salvador after Murphy's initial ruling. The judge said this month that if the military similarly flew migrants to Libya, that would "clearly violate" his ruling.