The two planes were already in the air, on their way to El Salvador and Honduras, when the decision to stop for 14 days came from a federal judge, according to government officials on Sunday.
The deportations are taking place after Trump invoked a war law from 1798 to be able to deport undocumented migrants. The immediate goal is to quickly deport members of a Venezuelan cartel that Trump believes has "invaded" the country.
The judge verbally ordered the planes to turn around, which did not happen, and that part is not even noted in the written verdict.
"Oops, too late", writes El Salvador's Trump-friendly president Nayib Bukele on X.
The country has an agreement with the US to receive migrants and put them in custody.
Foreign Minister Marco Rubio reports on X that more than 250 cartel members have been received by El Salvador.
The American authorities have not presented any evidence that the individuals are actually criminals.
The law, the Alien Enemies Act, is designed to be invoked when the US is at war and was last used during World War II.
