A federal judge says he is having second thoughts about his belief that the Trump administration was acting in good faith to comply with his orders to reunify families separated at the border.

The Justice Department on Friday filed a plan to reunify more than 2,500 children age five and older by a court-imposed deadline of July 26 using "truncated" procedures to verify parentage and perform background checks.

The procedures exclude DNA testing and other steps the administration took to reunify children under five.

U.S. District Judge Dana Sabraw took umbrage, disputing the administration's interpretation of his orders and saying that safe reunification can and must occur by July 26.

"So much of this is really common sense and common courtesy," Sabraw said. "Someone is making determinations as to who's getting reunified, what time and where. That information can be communicated. There shouldn't be anything mysterious about it. It should be transparent and easy to do."

The administration said the abbreviated vetting puts children at significant safety risk but is needed to meet the deadline.

The American Civil Liberties Union said the administration failed to meet last Tuesday's deadline to reunify dozens of children under five with their families and should, therefore, be closely watched as the next deadline approaches.

The administration disputed that characterization, saying it reunified all 58 children under five who were eligible and that it complied with the judge's order. The administration said 46 of the children were not eligible for reunification. The administration acknowledged that 20 of the children were reunited on Wednesday and Thursday, after the deadline.

Regardless of the reunifications, ACLU lawyers said, the government missed the court-ordered deadline and the lawyers would be deciding how to address the noncompliance with the court.

"If in fact 57 children have been reunited because of the lawsuit, we could not be more happy for those families. But make no mistake about it: the government missed the deadline even for these 57 children," attorney Lee Gelernt said.

Former U.S. Attorney Peter Nunez told Politically Speaking the challenges for the government begin when families decide to bring children across the border illegally. He says it’s a way to try to defeat American immigration law.

“So they’re playing the American public for suckers in a sense by using their children as sort of a get out of jail free card,” he said. “The only way to stop illegal immigration is to stop rewarding it, he added.

San Diego Congressman Scott Peters said the U.S. should to go back to the "catch and release" policies of the Obama administration.

“When someone comes through our doors for asylum because they’re fleeing political persecution or gang violence, we would process them through the regular due process, which just means that we would 'catch and release,'” he told Politically Speaking. “We can monitor them electrically. Under the Obama administration, we assigned caseworkers to families to make sure they came back. One hundred percent of them came back for their hearings. They’re not trying to flee the law, they’re trying to obey the law and have a better future and that’s the process we need to get back to.”

Last month, Sabraw gave the administration 14 days to reunify children under five and 30 days for children five and older - July 26. 

Making the reunification process more difficult, a dozen of the parents have already been deported. The administration said the deported parents are being contacted.

Parents and children were originally separated at the border because of the Trump administration’s zero-tolerance policy that requires prosecution of anyone who crosses the border illegally, which is a misdemeanor crime.