LOS ANGELES - A federal judge has praised the US government for reuniting 1,800 migrant children it took from their families at the Mexican border - but demanded that the focus shift to 400 who remain in custody because their parents have been deported.

Judge Dana Sabraw spoke out a day after it was revealed that hundreds of families had still not been reunited after being split under President Donald Trump's controversial "zero tolerance" policy against undocumented migrants.

Sabraw had ordered that all eligible migrant families be brought back together by 6:00 pm (2200 GMT) Thursday. Officials said in a court filing that while 1,820 children aged five and older were back with their parents, hundreds remained in custody.

The government insists the deadline has been met, as the families of those remaining are ineligible for a variety of reasons, including unconfirmed family ties or parents with criminal records.

Sabraw accepted that "the process has been completed" and said the government "deserves great credit in this regard" for making the deadline.

But he insisted that finding the deported parents must be the "the second stage." Stage three, said the judge, would be to set up a protocol ensuring that "this never happens again." The controversial separations began in May, when migrants illegally entering the United States were detained en masse, and their children taken to detention centers and shelters. Justice Department attorney Scott Stewart told the court there were 1,000 families with "executable" deportation orders - 400 of whom were in custody and would be the first removed.

Many others had been released from custody upon reunification, he added, but will be subject to deportation as soon as Sabraw lifts a stay on removal proceedings.

The American Civil Liberties Union, which brought the lawsuit to reunite the families, says the government is manipulating the figures to give a false impression.

"The Trump administration is trying to sweep them under the rug by unilaterally picking and choosing who is eligible for reunification," Lee Gelernt, of the ACLU, said in a statement.

"We will continue to hold the government accountable and get these families back together."

The organization wants reunited families to have a week to decide their next move, whether that be fighting for asylum, agreeing to go but leaving the children, or the whole family leaving together. Most are from Central America, fleeing gang violence and other turmoil.

The judge, based in San Diego, addressed the eligibility controversy by remarking that the government could only reunite children under its control. He postponed ruling on the seven-day delay request.

The separations triggered outrage in the US and abroad, especially after the release of audio of small children in shelters crying for their parents.

The pressure led to the Republican president demanding an end to the separations in June, six weeks after the "zero tolerance" policy kicked into high gear. Sabraw then ordered the reunifications, with Thursday as the deadline.

But the pace has been slow; children and parents are being housed in different parts of the country, while many adults have been deported.

Lawyer Efren Olivares of the Texas Civil Rights Project, which represents some parents, said the treatment of migrant families had been marked by "chaos and cruelty."

Last month, Sabraw ordered the government to return children under the age of five to their parents by July 10 and those between five and 17 by Thursday.

The government missed the first deadline. It deemed 45 children ineligible for return because their parents were not fit or able to take them.

As of Tuesday - before the latest figures were announced - the US Department of Health and Human Services had in its custody 11,500 children classified as unaccompanied aliens, mainly minors who entered without an adult.