AUSTIN — When a 15-year-old boy from Honduras ran away from a huge facility holding migrant children along the Mexican border in South Texas on Saturday, the staff ran beside him, pleading with him to stay. They said he would be safe, fed and have better luck being reunited with his family through the team at the former Walmart in Brownsville, Tex. — now known as Casa Padre — than if he went out on his own.

But the teenager, who had been outside during scheduled recreation time, fled the warehouse and went missing for more than 24 hours, raising questions from lawmakers about the welfare of children under President Trump’s zero-tolerance policy for those caught illegally crossing the border.

A Dallas man, who had originally falsely claimed to be the boy’s father, contacted Casa Padre officials to report that the boy had crossed into Mexico shortly after leaving the facility, according to a source familiar with the situation. The man told officials there that the teen was trying to travel back to Honduras.

Detective Jose J. Trevino of the Brownsville Police Department confirmed that the 15-year-old was reported missing by the center on Saturday. He said the teenager’s whereabouts were unknown and that authorities plan to review video evidence from bridges that lead from Brownsville to Mexico to see if he crossed, noting that there are other ways to cross that wouldn’t have been picked up by surveillance cameras.

The teen had been at Casa Padre for 36 days, said Jeff Eller, a spokesman for Southwest Key, which runs the shelter in Brownsville. The massive center, believed to be the largest in the country, houses more than 1,500 boys ages 10 to 17.

Before the teen ran away, authorities were in contact with the man in Dallas who claimed to be his father, but the center would not release the teen to the man after noticing that their birth certificates did not match up and finding discrepancies in a DNA test, according to a person with knowledge of the case.

Southwest Key said the teen is one of 42 who have left the program’s 26 shelters on their own since October 2017. Eller said such flight is rare; the program has housed nearly 20,000 children in Texas, Arizona and California.

The Brownsville shelter is licensed by the state and houses both those who crossed the border alone and those who were separated from their relatives under the Trump administration’s family-separation policy, which the president ended last week with an executive order.

Amid intense worldwide interest in the shifting U.S. immigration policies, Casa Padre reported the boy missing on Saturday afternoon. Police sent out search teams but were unable to locate him.

Facilities such as Casa Padre cannot forcibly prevent any children in their care from leaving, advocates say. Federal officials confirmed that the facilities can’t detain the children involuntarily; they have declined to respond to requests about how many children across the country have left such migrant centers.

“As a licensed child-care center, if a child attempts to leave any of our facilities, we cannot restrain them,” Eller said in a statement. “We are not a detention center. We talk to them and try to get them to stay. If they leave the property, we call law enforcement.”

Casa Padre staff are trained to talk children out of leaving.

“We walk or run beside them and tell them, ‘We can give you more help reuniting with your family. It’s safe here,’ ” said a source familiar with the situation who asked not to be named because he does not have permission to speak with the media.

Guadalupe Herrera, a former employee at Casa Padre, said Southwest Key employees were trained not to chase after children who ran when given the opportunity, such as on trips outside the facility: “They told us to take care of the group, and let the kid go.”

Though Southwest Key officials said it is rare that a child in their custody would flee, a boy who lived in Casa Padre said he saw several try to escape.

“They tried running toward the exits,” said Jairom, 17, an unaccompanied minor from Honduras who lived at Casa Padre from March until May, when he was placed with relatives in Maryland. “But they couldn’t figure a way out.”

The Rev. Anthony O’Connor, the pastor at San Felipe de Jesus Church in Brownsville, has spent the past five years ministering to children in shelters for unaccompanied minors. In May, he watched as a teenage boy visiting his church from Casa Padre for prayer service suddenly took off running. “One kid took a bolt from here,” O’Connor said. “He came out of the toilet and went straight for the door. There were supervisors there but he was so fast. They didn’t chase him, they just called ICE or Border Patrol.”

During a recent tour of Casa Padre, Southwest Key’s founder and CEO Juan Sanchez told reporters that some children had run away from the shelter but that it is unusual.

“Most of these kids know we’re trying to reunite them with their families,” Alexia Rodriguez, Southwest Key’s vice president of immigrant children services, told The Washington Post during the same tour. “So there is no reason to run away.”

Miller reported from Eloy, Ariz. Eli Rosenberg in Washington contributed to this report.