The written notice appeared in the case docket at 19:25 EDT on Saturday (00:25 GMT on Sunday), the Reuters news agency reports, although it is unclear when the flights carrying the alleged gang members departed from the US.
In a court filing on Sunday, Department of Justice lawyers said the order had not applied because the deportees "had already been removed from United States territory".
The justice department has appealed against the judge's ruling.
The American Civil Liberties Union, which was involved in the lawsuit against the Trump administration, said the court's order may have been violated.
The case raises constitutional questions since, under the US system of checks and balances, government agencies are expected to comply with a federal judge's ruling.
Venezuela criticised Trump invoking the Alien Enemies Act, saying it "unjustly criminalises Venezuelan migration" and "evokes the darkest episodes in the history of humanity, from slavery to the horror of the Nazi concentration camps".
Rights groups condemned Trump, accusing him of using a 227-year-old law to circumvent due process.
Amnesty International USA wrote on X that the deportations were "yet another example of the Trump administration's racist targeting" of Venezuelans "based on sweeping claims of gang affiliation".
President Bukele, a Trump ally, wrote that the detainees were immediately transferred to El Salvador's notorious mega-jail, the Terrorism Confinement Center (Cecot).
The El Salvadoran president said they would be held there "for a period of one year", and that could be "renewable".
El Salvador's Cecot jail is part of Bukele's effort to crack down on the country's organised crime.
The newly built maximum-security facility, which can hold up to 40,000 people, has been accused by human rights groups of mistreating inmates.
Shadowthron8 on March 16th, 2025 at 15:44 UTC »
We didn’t deport them to Venezuela though. We paid El Salvador to imprison them in some sort of work camp super max prison site situation
bet the range of people and dissidents exported here grows
SharksForArms on March 16th, 2025 at 15:34 UTC »
Fine, we can't arrest the president for giving illegal order? Arrest the people that carry them out.
zetia2 on March 16th, 2025 at 15:16 UTC »
How? I thought by avoiding shutdown the courts would still be functioning and they would stop Trump in his tracks. Schumer said so.
How can he just ignore the court orders, that's not following the rules. I guess no one could have anticipated that.