The US supreme court has ordered the Trump administration to temporarily halt the deportation of Venezuelan men in immigration custody, after their lawyers said they were at imminent risk of removal without the judicial review previously mandated by the justices.

“The government is directed not to remove any member of the putative class of detainees from the United States until further order of this court,” the justices said early on Saturday.

Conservative Justice Clarence Thomas publicly dissented.

The order is the latest example of how the country’s courts are challenging the Trump administration’s overhaul of the immigration system, which has been characterised by a number of deportations that have either been wrongful or carried out without due process.

In an emergency Friday court filing, lawyers for the American Civil Liberties Union (ACLU) said dozens of Venezuelan men held in Immigration and Customs Enforcement’s Bluebonnet detention center in Texas were given notices indicating they were classified as members of the Tren de Aragua gang. They said the men would be deported under the Alien Enemies Act (AEA), and were told “that the removals are imminent and will happen tonight or tomorrow”.

The ACLU warned immigration authorities were accusing other Venezuelan men held there of being members of the Tren de Aragua gang that would make them subject to deportation.

The ACLU said a number of the men in Texas had already been loaded on a bus and urged the court to rule before they could be deported.

The ACLU has already sued to block deportations under the Alien Enemies Act of two Venezuelans held in the Texas detention center and is asking a judge to issue an order barring removals of any immigrants in the region under the law.

The supreme court has allowed some deportations under the AEA, but has previously ruled they could proceed only if those about to be removed had a chance to argue their case in court and were given “a reasonable time” to contest their pending removals.

Federal judges in Colorado, New York and southern Texas have also issued orders barring the removal of detainees under the AEA until the administration provides a process for them to make claims in court. But there’s been no such order issued in the area of Texas that covers Bluebonnet, which is located 24 miles north of the city of Abilene in the far northern end of the state.

District judge James Wesley Hendrix this week declined to bar the administration from removing the two men identified in the ACLU lawsuit because immigration officials filed sworn declarations that they would not be immediately deported.

But the ACLU’s Friday filing includes sworn declarations from three separate immigration lawyers who said their clients in Bluebonnet were given paperwork indicating they were members of Tren de Aragua and could be deported by Saturday. In one case, immigration lawyer Karene Brown said her client, identified by initials and who only spoke Spanish, was told to sign papers in English.

“Ice informed FGM that these papers were coming from the president, and that he will be deported even if he did not sign it,” Brown wrote.

The ACLU asked Hendrix to issue a temporary order halting any such deportations. Later on Friday, with no response from Hendrix, the ACLU asked district judge James Boasberg in Washington to issue a similar emergency order, saying they had information that detainees were being loaded on buses.

In their court filing, lawyers say clients received a document Friday from immigration officials, titled “Notice and Warrant of Apprehension and Removal under the Alien Enemies Act”.

It reads: “You have been determined to be … a member of Tren de Aragua.”

“You have been determined to be an alien enemy subject to apprehension, restraint and removal from the United States … This is not a removal under the Immigration and Nationality Act,” the notice reads.

Before the supreme court decision, Pramila Jayapal, a Washington Democrat, denounced the reported plan. “We cannot stand by,” Jayapal wrote on social media, as the Trump administration “continues to disappear people”.