LOS ANGELES, United States (AFP) — The US government said Thursday that hundreds of families it broke up at the border with Mexico have not been reunited as a court-ordered deadline to return all children to their parents elapsed.

A federal judge in California had ordered that all eligible migrant families be brought back together by 6:00 pm and officials said in a court filing that 1,442 children aged five and older had been reunited with their parents.

“The reunification plan outlined to the court… is proceeding, and is expected to result in the reunification of all class members found eligible for reunification at this time by the court’s July 26, 2018 deadline,” the government said.

A further 378 children had already been released under other “appropriate circumstances,” the filing added, but more than 700 children remain in custody.

The government said the deadline had been met however, as those families were ineligible, either because family ties have not been confirmed, or the parent has a criminal record, a communicable disease or cannot be found.

The controversial separations began in May, when migrants entering illegally were detained en masse, and their children taken to detention centres and shelters.

The American Civil Liberties Union, which brought the lawsuit to reunite the families, said earlier Thursday that the government was manipulating the figures to give a false impression of success.

“These parents and children have lost valuable time together that can never be replaced. We’re thrilled for the families who are finally reunited, but many more remain separated,” Lee Gelernt, deputy director of the ACLU’s Immigrants’ Rights Project, said in a statement.

“The Trump administration is trying to sweep them under the rug by unilaterally picking and choosing who is eligible for reunification. We will continue to hold the government accountable and get these families back together.”

The deadline is seen as turning a page on the scandal, but the turmoil is barely beginning for many families that now face life-altering decisions, including whether or not to agree to long-term separations, rights advocates and lawmakers say.

Lawyer Efren Olivares of the Texas Civil Rights Project, which represents some parents, said the US treatment of migrant families had been marked by “chaos and cruelty,” and that officials’ rush to reunite parents and children lacked organisation.

As the deadline neared, dozens of families with children gathered for a sit-in on Capitol Hill, while Democratic lawmakers blasted President Donald Trump’s “zero tolerance” border policy as un-American.

The separations triggered outrage in the US and abroad, especially after the release of audio of small children in shelters crying for their parents, many of whom fled turmoil and gang violence in Central America.

The pressure led to the Republican president demanding an end to the separations six weeks later. Judge Dana Sabraw in San Diego then ordered the reunifications, setting 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.

Government data indicates that the parent or parents of more than 430 children may already have been deported, some of them voluntarily — enormously complicating any possible reunion.