A federal judge commended the Trump administration on Friday for the progress made reuniting families separated by the Department of Homeland Security's "zero tolerance" immigration policy, but blamed the administration for losing track of some migrant parents.

U.S. District Judge Dana Sabraw said that the Trump administration was "at fault" for deporting more than 400 parents while their children remained in custody, according to CBS News.

"The government is at fault for losing several hundred parents in the process and that's where we go next" in the process, Sabraw said.

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"Each [department] was like its own stovepipe, each had its own boss, and they did not communicate," he continued. "What was lost in the process was the family."

Sabraw faulted the government's lack of a plan to reunify families when the detainment program began as a key reason for the delay in family reunifications. The Trump administration faced Thursday a court order to reunify the remaining families.

More than 1,800 children had been reunited with their parents by Friday, the government said, but reported that hundreds more were deemed "ineligible" for family reunification. As many as 400 of the 711 children still detained may have had their parents deported already, CBS News reported.

Administration officials disputed the idea Friday that parents who were deported were not allowed to take their children with them, stating that in many cases parents declined to remove their children from Immigration and Customs Enforcement (ICE) custody.

"It’s been longstanding ICE policy to allow parents to take their children with them. Many parents declined this opportunity," said Matt Albence, head of ICE's enforcement and removal operations.

"The parents had the ability to change their mind," added Health and Human Services (HHS) Department spokesperson Chris Meekins, who said that if that happens, HHS works "expeditiously" to reunite them.