Migrant families line up to enter a bus station after they were processed and released by U.S. Customs and Border Protection on June 24. (David J. Phillip/AP)

Lawyers for the Trump administration on Friday asked a federal judge for more time to reunite immigrant children with their parents, the latest signal that the government is struggling to bring families back together after separating thousands as they crossed the U.S.-Mexico border earlier this year.

U.S. District Judge Dana Sabraw in San Diego ordered the government to return children younger than 5 to their parents by Tuesday, but federal lawyers said they could meet that deadline for only about half of the 101 children in that age group.

Officials say they have deployed hundreds of government employees and opened a command center usually reserved for natural disasters to match parents and children. But the massive effort is complicated by difficulty in locating some parents and, in other cases, uncertainty about the parents’ identities. Some parents have been deported and others have been freed in the United States, apparently without a system to monitor everyone’s whereabouts.

The judge ordered the government to deliver a list of the children’s names to the American Civil Liberties Union, which brought the lawsuit, by Saturday and said he would decide Monday whether to grant an extension.

“And then we can have a more intelligent conversation,” Sabraw said Friday at a status hearing on his order, adding that “then the court can determine whether it makes sense to relax the deadlines as far as reunification. But I would need more information.”

Friday’s hearing captured the frustrations over the Trump administration’s inability to get a handle on the number of parents separated from their children in recent months after implementation of President Trump’s “zero tolerance” policy at the border. It also foreshadowed the troubles officials could face as they try, over the next three weeks, to locate the parents of roughly 3,000 children ages 5 to 18. The deadline is July 26.

Sabraw, appointed in 2003 by President George W. Bush, late last month ordered federal officials to reunite all families within 30 days, and children younger than 5 within two weeks. Families were initially apprehended together, and then parents were sent to criminal jails after being charged with illegally crossing the border, or to civil immigration agencies to seek asylum or face deportation. Children were sent to shelters overseen by the Department of Health and Human Services.

In court records, the agencies said they were not prepared to track the separated parents and children, which partly delayed their efforts to reunite them.

A Justice Department lawyer told the judge Friday that reunions should happen swiftly for approximately half of the 101 children younger than 5 who are being held in shelters.

“There are then some groups for whom the reunification process is more difficult,” lawyer Sarah Fabian told the judge. “In some cases if we’re not, for example, aware of where the parent is, I can’t commit to saying that reunification will be able to occur by the deadline.”

Acknowledging that the numbers were in flux, she said the government had matched 86 parents to 83 children. Sixteen children had not been matched, and it remained unclear whether they crossed with their parents, she said. About 46 parents are in immigration custody, 19 were deported and 19 were released. Nine others are in the custody of U.S. marshals.

Two parents had criminal records that made them ineligible to regain custody of their children, Fabian said, noting that the figures she outlined were not a full accounting and that efforts to match families are ongoing.

Lee Gelernt, a lawyer with the ACLU who brought the class-action lawsuit on behalf of parents separated from their children even before the administration’s “zero tolerance” policy took effect in May, told Sabraw that the government’s lack of record-keeping was “startling.”

“It just doesn’t make sense,” he said. “You’ve taken a child from a parent. They need to give the child back.”

Gelernt urged the judge to require the government to stick to the deadlines and said that thousands of lawyers are willing to help match parents with their children, which is why he asked the Justice Department for a list.

A parallel lawsuit, brought last month by the Democratic attorneys general of 17 states and the District of Columbia, also seeks the rapid reunification of separated families. This week, the states asked a federal judge in Seattle to expedite discovery in the case, arguing that the government has not turned over key information — about its policies, separated families, and asylum seekers refused entry into the country — in response to repeated requests from state officials.

The states also argued that they need to gather testimony from migrant parents and children who are in federal custody and could be moved to different detention centers at any time. “Many of the key witnesses will likely be moved in the coming days and weeks with no assurances as to their well-being or whereabouts, and continued chaos is inevitable,” their motion says.

The motion includes hundreds of pages of sworn declarations from migrant parents and their advocates detailing alleged experiences that mothers, fathers and children have endured while trying to seek asylum in the United States. In one account, a 14-month-old baby fleeing El Salvador last year was separated from his father at a port of entry in Southern California. His mother, Olivia Caceres, sought asylum weeks later and — after enduring one bureaucratic hurdle after another, including a DNA test — was reunited with her son nearly three months after he was taken away. He was “full of dirt and lice,” Caceres said in her declaration. “It seemed like they had not bathed him the 85 days he was away from us.”

The child, identified only as “M.,” now cries inconsolably and is afraid to be alone, she said. “M. is not the same since we were reunited,” Caceres said.

Advocates for immigrants have blasted the Trump administration, suggesting officials have created bureaucratic obstacles to delay the reunions. Authorities say they are conducting DNA testing and background checks to protect children as required by a bipartisan anti-trafficking law enacted in 2008.

Susan Church, a Boston immigration lawyer, said the government could release migrants who are seeking asylum on bond so that they can find their children faster. She represents a Guatemalan woman who had an emotional reunion with her 8-year-old daughter this week after being separated for 55 days.

The girl turned 8 in a government shelter.

“I can’t believe they have the nerve to ask for more time,” Church said. “It’s outrageous. The government has a choice here, and that choice is to release people on bond and then reunification could happen immediately. But they’re choosing not to do that and asking the court for more time.”

A Justice Department spokesman declined to address questions seeking clarity on the administration’s desired timeline to reunite families. In a statement, an administration official said its priority was “to ensure the safety of the children in its custody.”

Dozens of government workers have descended on child shelters and immigration jails to conduct interviews and collect forms. But court records reveal the challenges ahead.

Robert Guadian, a senior official with U.S. Immigration and Customs Enforcement (ICE), called the process “difficult and time consuming” in court documents filed Friday. ICE detains parents for deportation but does not track whether they have been separated from their children, he said, noting that the parents of children younger than 5 are scattered in 23 immigration jails across 13 states.

Although all detained parents had spoken by phone to their children as of Friday, as Sabraw ordered, Guadian said officials still must complete criminal background checks on the parents.

Immigration officials said they have relocated 23 parents to facilities that are closer to the HHS shelters where their children are staying.

ICE is attempting to match many more parents to older children, who the judge said must be reunited within 30 days. Officials said the agency has completed approximately 300 background checks, which include criminal and immigration histories, but still has 1,400 to finish.

Emma Brown contributed to this report.