Donald Trump's administration has taken credit for meeting a court-ordered deadline to reunite thousands of migrant families it separated at the border — despite hundreds of children remaining apart from their parents.

More than 700 migrant kids have not been reunified with their parents since the White House launched a "zero tolerance" policy along the US-Mexico border. That policy began the systematic separation of families, including those legally seeking asylum, forcing children into immigrant detention centres and makeshift “tent cities.”

The administration said it reunified all eligible migrant children — nearly 1,800 — with their family members by Wednesday’s 6.00 p.m. deadline, claiming the more than 700 outstanding cases could not be resolved due to outside circumstances.

In some instances, children could not be reunited due to a parent or guardian’s criminal record or suffering from a communicable disease. However, in the majority of cases, families have not yet been reunited because the parent was deported or left the country without their child.

At least 431 cases involved parents that were no longer in the US after being separated from their kids at the border, according to Wednesday’s court filing.

Guatemalan migrant Maria del Carmen Tambriz reacts after being returned from the U.S. without her daughter after they were separated by U.S. border officials in Guatemala city, Guatemala, July 26, 2018. (Reuters)

Another 120 include parents allegedly signing paperwork to "waive reunification." The American Civil Liberties Union (ACLU), which sued Mr Trump’s administration over its zero tolerance policy, has expressed concern that some of those parents may have been coerced or unaware of what they were signing.

"One father was told that if he didn’t sign the form presented to him, then he would not see his daughter again," Kathryn Shepherd, a lawyer with the ACLU, wrote in a court affidavit.

Mr Trump's administration previously failed to meet an earlier deadline to reunify migrant children under the age of five-years-old with their families, though it now claims to have fulfilled that order.

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Of those 100 toddlers, 57 were reunited with their parents while 46 were deemed ineligible for similar claims in the latest court filings.

Still, the federal government has said it met all legal requirements put forth by US District Court Judge Dana Sabraw, who ordered the reunification deadlines.

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"By the court deadline this evening we are on track to reunite all eligible parents within ICE custody," Department of Health and Human Services’ (HHS) Chris Meekins said in a statement on Thursday.