Maria holds her 4-year-old son Franco after he arrived at the El Paso International Airport Thursday, July 26, 2018 in El Paso, Texas. The two had been separated for over six weeks after being entering the country. (Ruben R. Ramirez/The El Paso Times via AP)

Maria holds her 4-year-old son Franco after he arrived at the El Paso International Airport Thursday, July 26, 2018 in El Paso, Texas. The two had been separated for over six weeks after being entering the country. (Ruben R. Ramirez/The El Paso Times via AP)

SAN DIEGO (AP) — A federal judge commended the Trump administration for reunifying families in its custody with their children after being separated at the U.S.-Mexico border, while faulting it for leaving hundreds of families still apart and warning that a better system must be in place.

U.S. District Judge Dana Sabraw said the government gets “great credit” after reunifying more than 1,800 children 5 and over with parents or sponsors by Thursday’s court-imposed deadline.

He pointed out that many of the families were reunited while in custody then turned his attention to 431 children whose parents have been deported.

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“The government is at fault for losing several hundred parents in the process and that’s where we go next,” the judge said.

Sabraw ordered the government and the American Civil Liberties Union, which represents the parents, to submit written updates every Thursday on still-separated families.

The order signaled slightly looser oversight than Sabraw imposed last month with frequent hearings to make sure his deadline was met.

In late June, the judge gave the government 14 days to reunify children under 5 and 30 days to reunite children 5 and older with their families.

Sabraw said the “problem” could not be repeated, describing how Homeland Security, Health and Human Services and Justice departments didn’t have a system to keep track of the families that were separated when the administration introduced a “zero tolerance” policy toward illegal entry.

“Each (department) was like its own stovepipe, each had its own boss, and they did not communicate,” he said. “What was lost in the process was the family.”

Sabraw didn’t rule immediately on a request by the ACLU to give parents a week to decide whether or not to seek asylum after the group is notified that the family is reunited. As a result, a temporary halt on deportations remained in place.

Earlier Friday, Homeland Security officials said they had reunified all eligible parents with children — but noted many others were not eligible because they had been released from immigration custody, are in their home countries or chose not to be reunited.

More than 1,800 children 5 and older had been reunited with parents or sponsors as of Thursday. That included 1,442 children who were returned to parents who were in U.S. Immigration and Customs Enforcement custody, and another 378 who were released under a variety of other circumstances.

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On a parallel legal front, a federal judge in Los Angeles said Friday that she will appoint an independent monitor to evaluate conditions for immigrant children in U.S. border facilities in Texas following a spate of reports of spoiled food, insufficient water and frigid conditions faced by the youngsters and their parents.

Judge Dolly M. Gee said she reached her decision after seeing a “disconnect” between U.S. government monitors’ assessment of conditions in facilities in Texas’ Rio Grande Valley and the accounts of more than 200 immigrant children and their parents detailing numerous problems.

“It seems like there continue to be persistent problems,” she said during a hearing on a longstanding settlement in a case focusing on the care of children in government custody. “I need to appoint an independent monitor to give me an objective viewpoint about what is going on at the facilities.”

Peter Schey, an attorney who represents immigrant children detained by the U.S government, said problems have worsened with children now spending three to six days in U.S. Customs and Border Protection facilities, where they were previously held one to three days.

“We’ve seen an intensification with all the chaos the administration has caused,” said Schey, who has long requested an independent monitor.

Sarah Fabian, a Justice Department attorney, opposed the appointment without having an opportunity to respond to the accounts of children and parents collected by immigrant advocates at facilities in June and July. She said border authorities, for example, provide water fountains and jugs in cells and that facility conditions must comply with agency policies.

Both sides have until Aug. 10 to agree on a proposed monitor. If they can’t, each will make suggestions to the judge and she will choose.

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Long reported from Washington and Taxin reported from Los Angeles.