The Trump administration said Thursday it would meet a court-ordered midnight deadline to reunite “all eligible parents” who were separated from their immigrant children at the Mexican border.

Officials said 1,442 kids out of some 2,500 had been returned to parents who being held by immigration agencies as of about 6 p.m. Thursday and more would be over the next several hours.

Another 378 were released under “other appropriate circumstances,” including to a parent inside the United States or to an eligible sponsor.

“By the court deadline this evening [midnight West Coast time] we are on track to unite all eligible parents within ICE custody,” said Chris Meekins of the Department of Health and Human Services.

That left 711 kids still in HHS custody because their parent was considered “not eligible” or “not available” — including 431 whose parents who are now outside the United States, 46 parents whose had a “red flag” in their case file and 21 parents who flunked criminal-background checks.

Gov. Cuomo, speaking earlier, blamed the feds’ “incompetence” and “malice” for the fiasco and shared a harrowing anecdote about an ordeal children sheltered in New York faced overnight Wednesday.

The feds, he said, sent a list of 80 children to the Cayuga Center in East Harlem, telling officials there to have the children “be ready to fly out in several hours.”

But most of the youngsters weren’t even staying at Cayuga, he said, so the feds sent a second list with 14 names and told the center to take them to La Guardia Airport.

“Only seven of 14 had flights, so there were seven left,” Cuomo said.

The Cayuga officials were then told to drive the seven to Westchester County Airport — “but only two had tickets,” Cuomo added.

“The remaining five went back to Cayuga after being driven around all night. This is gross incompetence and chaos on the part of the federal government. It’s despicable and it’s illegal.”

Meanwhile, lawyers and advocates complained of miscommunication and lack of coordination as the government shuttled children from around the United States to detention centers in the Southwest, where many parents were being held.

“We’re seeing some kids swept away in the middle of the night to be reunified,” said Anthony ­Enriquez of Catholic Charities of New York, which represents some of the affected children.

Mayor de Blasio said social-service providers told the city that about 200 children detained locally had been moved out by federal officials and that about 100 remain, “with no end in sight for them.”

It’s unclear what happens to kids whose parents have already left the United States or whose parents are deemed ineligible for reunification.

“We’re in uncharted ‘no man’s land,’ ” said Ur Jaddou, former chief counsel to the federal US Citizenship and Immigration Services who serves as director of the advocacy group DHS Watch.

With Post wires