(WASHINGTON) — A federal judge is probing whether the Trump administration deported migrants to South Sudan on Tuesday in violation of an earlier order barring deportations of migrants to countries other than their own without giving them sufficient chance to contest their removal.

An order from U.S. District Judge Brian Murphy late Tuesday directs the government to “maintain custody and control” of anyone deported to South Sudan covered under a lawsuit challenging the administration’s practice of deporting migrants to third countries “to ensure the practical feasibility of return if the Court finds that such removals were unlawful.”

The judge’s order comes after attorneys with the National Immigration Litigation Alliance and other groups filed an emergency motion to bar the government from deporting migrants to South Sudan, saying they had indications at least 12 migrants had been sent to the East African country.

Lawyers said they believed one of the men, a native of Myanmar identified in court filings as “N.M.,” was removed from the Port Isabel Detention Center in Texas to South Sudan on Tuesday morning. The attorneys also allege a Vietnamese migrant referred to as T.T.P. “appears to have suffered the same fate.”

Both men named in the filing have orders of removal to their home countries, the attorneys said.

During a hastily arranged virtual hearing Tuesday in U.S. District Court in Boston, a Justice Department lawyer told the judge that N.M. had been deported to Myanmar, not South Sudan. But the lawyer declined to say where T.T.P had been sent, saying the information was classified, according to an account of the hearing in The New York Times.

The lawyer also said the current location of the plane carrying the migrants to be removed as well as its final destination were classified, according to the Times.

Murphy, a Biden appointee, told the DOJ lawyer that officials who carried out deportations in violation of his earlier order could face criminal contempt proceedings, according to the Times. Attorney Trina Realmuto, of the National Immigration Litigation Alliance, who was present for the hearing, confirmed this account.

ABC News has reached out to DHS for comment about the alleged removals to South Sudan.

As a part of his order, Murphy also instructed the government to be prepared to identify the affected deportees and to provide more details about their removal and the opportunity each individual had to raise a fear-based claim.

The U.S. State Department currently advises American travelers not to visit South Sudan due to the threat of crime, kidnapping and armed conflict.

Another hearing in the case is set for Wednesday at 11 a.m.

Last month, Murphy issued an order requiring the Trump administration to provide individuals with written notice before they’re removed to a third country and a “meaningful opportunity” to raise concerns about their safety. The preliminary injunction also prohibits the government from removing a migrant to a third country without screening for possible risks to their safety in that country and a 15-day window to contest the government’s determination based on that screening.

In a declaration, one of the attorneys for N.M. said he was also one of the men whom the Trump administration attempted to deport to Libya earlier this month setting off a legal scramble to block it. In that instance, the judge said removing the men to Libya without due process would “clearly violate” his order.

ABC’s Jack Moore contributed to this report.

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