Nearly 500 children are still separated from their migrant parents nearly two months after a federal judge ordered the youngest to be returned to their family members and more than a month after the reunification deadline for older children.

Documents filed in a lawsuit seeking to reunite the families say 497 of the 2,654 migrant children that the Trump administration took from their parents at the border are still in federal custody and not with parents. Parents of 322 of those children were deported.

Judge Dana Sabraw ordered all children under age 5 to be reunited with parents by July 10, but 22 of them are still separated, according to government documents filed Thursday. The deadline for reuniting 5- to 18-year-old children was July 26.

On Friday, Rep. Joaquín Castro, D-Texas, called for a federal judge to take the reunification process from the Trump administration and appoint a special master or committee of special masters to oversee it.

The special masters would be able to use all the government resources to do the job, he said.

“The Trump administration started separating young kids from their parents with no plans to reunify them and that’s what makes this especially cruel. Some of these kids are very young and they’ve now been there for months and months,” Castro said on MSNBC’s "Morning Joe."

The president could appoint what amounts to a special master, but “this is just not a priority for him — this is not something he’s thought a lot about,” said Castro, who toured a Texas facility where separated children have been housed.

“It’s going to take the court, a judge, in this case, to come in there and say to Health and Human Services and to ICE (Immigration and Customs Enforcement), ‘I’m taking it out of your control. I’m giving it to somebody outside of government’ to make sure it gets done,” he said.

A Department of Homeland Security official declined to comment on the updated numbers and Castro’s statement citing pending litigation.

The Trump administration began separating children from parents and guardians to enforce its “zero tolerance” policy, which set a goal of 100 percent prosecution of people who crossed the border illegally, regardless of whether they had requested asylum or were eligible to apply for it.

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The children have been placed in facilities and kept in federal custody. There have been a number of complaints of sexual, physical and verbal abuse, mistreatment and the use of psychotropic drugs at shelters where children have been held. In Phoenix, a man working in a shelter there was arrested on suspicion of sexually abusing a 14-year-old girl.

'Get us out here'

On Thursday, four children held in custody at Karnes detention center, where fathers and their sons are being held, four children pleaded for freedom and to be liberated after being re-separated from their fathers.

Lawyers for RAICES, an advocacy and legal assistance group for immigrants and others in Texas, said that the fathers had been re-separated from their sons after some peaceful protests at Karnes. Several of the fathers had staged sit-ins, refused to eat, refused to follow ICE orders or to use their services to protest their jailing, RAICES officials said.

Participating in a conference call from the detention center, the children said repeatedly that the re-separation had made them sad. The children had been previously separated from their fathers. One child said he was separated for about two months from his father.

The children said through a translator that they were in school and officials came and took them to “medical” and were kept locked up in a room. At that time, they were separated again from their fathers and were not allowed to go to school for the day and a half they were separated.

One child also wanted to judges to know he was having trouble eating because of his sadness. Another child said he wanted to be released from the center so he could go to school and study.

The children, who were from Honduras and Guatemala, said they wanted to be freed with their fathers.

One child who was separated from his father, was reunified, separated again for a day and now remains held with his father in a detention center in Karnes, Texas, issued an appeal to President Donald Trump and ICE on Thursday on a media conference call from the center.

“I want to send a strong message to Donald Trump and to ICE: Get us out of here. We want our freedom,” the child said through a translator.

The administration’s breakdown of the children and their situations, included in court filings, shows that 497 children have parents considered not “eligible” for reunification or who are not “available.” Some parents have been red-flagged for potential criminal pasts.

The documents state that 322 children’s parents are not in the U.S. and 167 parents have “indicated desire against reunification, including a significant number who are not in the U.S.

But the ACLU has been arguing that a number of parents were coerced or misled by the government into giving up their right to seek asylum.

“These incidents include parents who were told that they needed to accept removal and not pursue asylum in order to be reunited with their children and parents who were required to sign documents they did not understand, in languages they do not speak that had the effect of waiving their right to seek asylum,” the documents state.

The continued separations are spilling into midterm elections, which will ramp up after the Labor Day weekend. Early voting starts in many states in October.

Castro said immigration is playing a big role in the contentious race between Sen. Ted Cruz, R-Texas, and Democratic challenger Rep. Beto O’Rourke, who an NBC News/Marist poll shows trails by 4 percentage points.

“Ted Cruz won’t stand up to Donald Trump even though … Donald Trump has done things that are hurting the state of Texas,” Castro said.

The child separations have been widely unpopular with Americans, although a recent poll showed support for removing the families and detaining them together.

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