A federal judge said Friday it is the responsibility of the Trump administration to reunite the hundreds of children separated from parents who have been deported to countries south of the border.

U.S. District Judge Dana Sabraw of San Diego said in a conference call Friday that for every parent who is not located, there will be a "permanently orphaned child, and that is 100 percent the responsibility of the administration."

The comments came after the Trump administration called on the American Civil Liberties Union (ACLU) to use its “considerable resources” to reunite children.

An increase in the number of children separated from their parents followed the Justice Department’s implementation of a “zero tolerance” policy that ordered the prosecution of all illegal border crossers.

Since then, President Trump has signed an executive order ending the practice of child separation, and the administration has been scrambling to reunite children with the appropriate parents or guardians.

The administration said last week that it had returned all 1,800-plus children and sponsors who were “eligible” for reunification, but that 700 adults were not eligible for a number of reasons. Those include that they had chosen not to be reunited, had already been released, were in their home countries, or had red flags for criminal records or something else.

TRUMP ADMINISTRATION SAYS ACLU SHOULD WORK TO REUNITE CHILDREN WITH DEPORTED PARENTS

The Associated Press reported that 410 children whose parents were outside the country were in the custody of Health and Human Services as of Wednesday.

The ACLU had demanded that parents who want their children sent to them be reunited within a week. Meanwhile it says that those who wish to return to the U.S. for their children should have round-trip transportation paid by the government.

But the Trump administration said the ACLU should do it instead. “Plaintiff’s counsel should use their considerable resources, and their network of law firms, NGOs, volunteers and others, together with the information that defendants have provided (or will soon provide), to establish contact with possible class members in foreign countries.”

The parents are predominantly in Guatemala, El Salvador and Honduras, and the State Department has begun talks with foreign governments on how to aid the reunification effort.

The ACLU said that it was the government's responsibility, not its own. It also noted that “there is no blueprint for finding deported parents.”

"Plaintiffs have made clear that they will do whatever they can to help locate the deported parents, but emphasize that the government must bear the ultimate burden of finding the parents," the ACLU said in its filing, blaming the crisis on the administration.

The Associated Press contributed to this report.