BROWNSVILLE, Texas -- A teenage boy who crossed the southern border unaccompanied recently has gone missing from the shelter where he was housed after being taken into custody, officials confirmed to CBS News.

The 15-year-old had been living at the Casa Padre shelter for unaccompanied minors in Brownsville, Texas. The facility is a former Walmart that has been retrofitted to house more than 1,000 youths transferred from the Department of Homeland Security (DHS) to the Department of Health and Human Services (HHS).

Southwest Key Programs is the company contracted by HHS' Office of Refugee Resettlement (ORR) to operate the Casa Padre facility, one of 26 shelters it oversees in Texas, Arizona and California. In a phone call with CBS News, spokesman Jeff Eller said 42 children have decided on their own to leave and not return to Southwest Key facilities since Oct. 1. He said the children typically climb a fence. Eller noted that the number of children who have gone missing accounts for just 0.21 percent of the 19,846 children the organization has cared for during that time.

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A source familiar with the situation told CBS News the boy was outside in a playground during scheduled recreational time Saturday when he "took off and climbed the fence." Facility staff did not try to restrain the boy, though they did briefly attempt to convince him to stay.

The ORR policy manual notes that child care providers must ensure each facility has "controlled entry and exit from the premises to ensure unaccompanied alien children remain within the facility perimeter."

However, Eller said in an earlier email that the child left of his own accord, and that the non-profit's employees were not allowed to stop him.

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

Eller said the child was reported missing to local authorities.

The boy arrived alone at the border recently, according to an HHS spokesperson. His father lives in the United States and is in the process of being vetted to be the boy's sponsor.

"When an (unaccompanied alien child) is reported as missing, local authorities, the Department of Homeland Security, and the UAC's Parent (or emergency contact) are notified. When a UAC is found, the UAC will be returned to DHS custody and most likely referred back to HHS until a suitable sponsor is found," the agency said in a statement emailed to CBS News.

Local and federal officials are searching for the boy, the spokesperson said.