President Donald Trump’s administration has reunited just more than half of 103 immigrant children under the age of 5 with their parents, though the rest remain in federal shelters for various reasons, including for safety concerns or because their parents have already been deported.

The government’s announcement Thursday comes two days after it missed a federal judge’s deadline to reunify the youngest category of up to 3,000 children who were separated from their parents at the southern border under the administration’s crackdown on illegal immigration.

DARK SECRETS: Unmarked vans, security fences: Family reunification shrouded in secrecy

Trump, facing growing furor over the hardline policy, suddenly ended the practice last month, but most parents and children remained separated until the judge, Dana M. Sabraw in San Diego, imposed strict deadlines as part of a lawsuit filed by the American Civil Liberties Union.

Now Playing: Now Playing Mayors Accuse Trump of Humanitarian Crisis Associated Press

Melania Trump visits Texas detention centers housing migrant children Los Angeles Times

Doc Says Immigrant Children Still At Risk Associated Press

More than 1,000 people march on El Paso immigration center San Antonio Express-News

States Plan to Sue Over Family Separation Associated Press

Nielsen at Capitol Ahead of Immigration Vote Associated Press

Hundreds March To Texas Tent City Holding Detained Immigrant Kids Time

Laura Bush condemns separating immigrant families Fox4

WH: 'Very Biblical to Enforce the Law' Associated Press

Lawmakers Call Administration Policy Child Abuse Associated Press

Trump Administration Denies Border Separation Policy Despite Published Proof Veuer

Republicans Decry Border Separation of Children and Parents as White House Defends It Time

Border Policy Defended Amid Protests Associated Press

Donald Trump Blames Democrats for Family Separation At the Border Fortune

DHS: About 2,000 minors separated from families KTVU

Pelosi: Separating Families at Border 'Barbaric' Associated Press

Sessions Cites Bible Backing Immigration Policy Associated Press

Congressional Democrats challenge Trump immigration policy Fox4

United Nations Asks U.S. To Stop Separating Migrant Children From Their Familes Time

Trump Talks Manafort, Cohen, Immigrant Children Associated Press

Honduran Man In U.S. Custody Kills Himself After Being Separated From Family at Border: Report Buzz 60

Protests over separating children from parents at border KTVU

Dozens rally to protest policy separating kids from parents at the border Fox4

Five Dead After a Border Control Chase Ends With a Crash in South Texas Time

Raw: Suspected Smuggling Vehicle Fatal TX Crash Associated Press

Report: Hundreds of Children Have Been Separated from Parents at the US-Mexico Border Veuer

WH: Joe Scarborough’s Comparison Of U.S. Border Policy To Nazis Is ‘Appalling’ GeoBeats

Dems: Separating Families at Border is Inhumane Associated Press

In the joint statement, Health and Human Services Secretary Alex Azar, Homeland Security Secretary Kirstjen Nielsen, and Attorney General Jeff Sessions said the agencies have worked “tirelessly” to reunite the children and praised their own vetting procedures for preventing the return of minors to dangerous situations.

“The Trump administration does not approach this mission lightly, and we intend to continue our good faith efforts to reunify families,” the officials said.

But the glacial pace and chaotic manner of the reunification efforts suggests ongoing difficulty as the government struggles to reunify the remaining thousands of children by its next deadline on July 26.

“We will be asking the court to even more closely monitor the government going forward and for it to provide more information on a regular basis,” said Lee Gelernt, a lawyer with the ACLU. A hearing is scheduled Friday, in which the ACLU will also ask the government to pay for counseling to treat children and reimburse families for travel costs and DNA testing.

HEART-WRENCHING: Immigrant mother separated from daughters reaches out in letter

The government said it had reunified 57 separated children in government custody who are under the age of 5, including six in San Antonio, but deemed another 46 “ineligible for reunification.” Of those, 22 children could not be reunited, either because their parents have criminal backgrounds or face criminal allegations, or because they were not children of the person with whom they crossed the border. One parent had a communicable disease. Another 12 parents have been deported and 11 remain in federal or state custody for other offenses.

One child, who would qualify for U.S citizenship because Gelernt said his mother is American, has been in federal foster care for more than a year. The government said the parent’s location is “unknown.”

“That opens up the reality that there are likely many U.S. citizen children who have been separated from their parents,” said Michelle Brané, director of migrant rights at the Women’s Refugee Commission, a national advocacy group.

In at least one other case, she said an American child had been separated from his family at the border and sent to a state welfare agency because he did not qualify for placement with the Office of Refugee Resettlement., which is charged with the care of immigrant children.

PRESSURE IS ON: Government moves fitfully, secretly to reunite surrendered immigrant families

Brané said the government is working from a list of separated children whom it had in its custody on the date of the judge’s order in late June. But hundreds more likely had been split from their parents and released to a relative or family friend before that decree was issued.

“It’s a very incomplete list of parents,” she said. “It’s not the total number of children who have been separated by any means.”

She urged the government to hasten the process and more proactively search for separated families.

“Otherwise we’ll end up with some families who are never reunified,” she said, because the government did not identify them as separated and it might be difficult or impossible to later find either parents or children.

Thousands of children 5 and older remain apart from their parents, and advocates say the process so far does not bode well for the next deadline.

“We’re not too heartened by it,” said Zenén Jaimes Pérez, a spokesman for the Texas Civil Rights Project, which has tracked 381 parents separated from their children.

Of those, he said six have been deported and have not been found. Another 17 have been released, usually on bond and with ankle monitors, and reunited with their children. Eight are being held with their children in family detention centers. The remainder are still detained alone, the vast majority at the Port Isabel detention center near Brownsville.

DESPERATELY SEARCHING: Separated immigrant families struggle to find each other amid border chaos

Pérez said it was unclear what the next stage of the reunification process would look like and whether many parents and children would simply be held together in two family detention centers near San Antonio while the government expedites their deportation cases.

Another California federal judge, Dolly Gee, this week rejected the administration's request to detain immigrant families for longer than several weeks, calling it a "cynical attempt" to undo a longstanding court settlement, known as the Flores agreement, which, among other things, limits to about 20 days the time children can be held in federal detention.

Lawyers say many separated parents are seeing their asylum cases dismissed, with bureaucrats denying many of the credible fear interviews, which is the first step to obtaining the protection.

“Everyone is getting denied,” said Carlos Garcia, a McAllen lawyer on the board of directors for the Texas Civil Rights Project. “There are not that many people getting positive credible fear interviews.”

Late Wednesday, the government issued stricter guidance to asylum officers to reject claims based on fears of gang and domestic violence. The orders follow a controversial ruling from Sessions last month that made it nearly impossible to gain asylum through such avenues, a predominant way for Central Americans seeking protection.

“(Wednesday’s) memo incorrectly instructs asylum officers to deny domestic violence and gang-related claims as a matter of course, when the law requires those claims to be reviewed on a case-by-case basis,” said Anastasia Tonello, president of the American Immigration Lawyers Association, in a statement. “Our nation cannot turn its back on such horrors in the way this policy instructs (asylum) officers to do.”

Even parents with strong cases are jeopardizing their claims because they are so anxious to reunify with their children, said Brané, of the Women’s Refugee Commission.

“Their focus is so, so desperate, specifically to being reunited with their children and worrying about their children that they can’t even think about other things,” she said.

In some cases, lawyers say separated parents are coerced into abandoning asylum claims and agreeing to deportation.

A Houston federal judge on Thursday ordered the government to halt its speedy deportation of a Honduran mother who faced horrific abuse at the hands of her ex-partner, a former police officer.

He raped her several times and threatened to kill her, according to legal filings.

The woman came here last month seeking protection but was imprisoned and her 12-year-old daughter placed in a federal shelter in Florida.

The mother failed her initial credible fear interview, but requested an immigration judge review the denial, as is allowed by law, said Leslie Thorne, a partner with Haynes and Boone who is handling the case.

Instead, Thorne said an official at the Port Isabel detention center “forced” the mother to sign a statement waiving that right, making her eligible for immediate deportation. The form was in English, which she does not understand.

“She was told to sign it and that she would be penalized if she did not sign it,” Thorne said.

The lawyers similarly requested a judge’s review but did not receive a response. They argue the mother’s due process rights were violated.

Chief U.S. District Judge Lee H. Rosenthal ordered the government temporarily pause her deportation for 14 days or until “certain conditions are met.”

Reporter Elaine Ayala contributed to this report.

lomi.kriel@chron.com

@lomikriel