Mothers and children wait to be assisted by volunteers in a humanitarian center in the border town of McAllen, Texas, July 5, 2018. (Photo:VCG)

US government on Thursday says more than 1,800 children that were separated at the US-Mexico border have been reunited with parents and sponsors but hundreds still remain apart. 

More than 700 parents were declared not eligible or currently not eligible, many of whom may have been deported, and their children remain in custody.

The American Civil Liberties Union, which brought the case against the government, said the data showed "dozens of separated children still have not been matched to a parent."

Immigration advocates said the government's push to meet the court's deadline to reunite families was marred by confusion and one said children had disappeared into a "black hole."

Maria Odom, vice president of legal services for Kids in Need of Defense, said two children who were represented by the group were sent from New York to Texas to be reunited with their mother. When they arrived, they learned their mother had already been deported, she said.

Odom said her group cannot find the children, aged 9 and 14.

It was an example, she said, "of how impossible it is to track these children once they are placed in the black hole of reunification."

The US Department of Homeland Security did not immediately respond to a request for comment.

The Trump administration's "zero tolerance" policy toward illegal immigration led to the separation of about 2,500 children while their parents, some asylum seekers, went through a legal process.

An outcry at home and abroad forced US President Donald Trump to order a halt to the separations in June. US Judge Dana Sabraw in San Diego ordered the government to reunite the families and set Thursday as the deadline.

Sabraw has criticized some aspects of the process, but in recent days, he has praised government efforts. As of Monday, 900 people had received final orders of removal, and civil rights groups said they must decide if they want to return home as a family or leave their child in the US to fight for asylum separately.

Government lawyers told a federal judge this week that 917 parents may not be eligible for prompt reunification because they have already been deported, have waived reunification, have criminal backgrounds, or are otherwise deemed unfit. The group included 463 the government said are no longer in the US.

Rights activists said some may have been coerced or misled into returning home, believing it was the only way to see their children. Government officials have said everyone in an immigration detention center has been given notice of their rights and contact information for a lawyer.

One immigrant, Douglas Almendarez, said he believed that returning to Honduras was the only way to be reunited with his 11-year-old son.