Det. J.J. Trevino of the Brownsville Police Departmenttold ABC affiliate KRGV that officers were called to the center in Brownsville on Saturday after the boy was reported missing from the Southwest Key Casa Padre location.
"As a licensed child care center, if a child attempts to leave any of our facilities, we cannot restrain them," Jeff Eller, a spokesman for Southwest Key, told ABC News. "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."
Neither caretakers nor authorities released the boy's identity but his information was entered into the missing children's database.
A source familiar with the case told ABC News the boy arrived at the shelter 36 days after he was caught crossing the border on his own.
A man reached out to officials at the center claiming to be the boy's father, the source said. But a DNA test showed the man was not the boy's biological parent, the source said.
After the teenager left the facility, the man called the center again to inform officials that he had heard from the boy, who was alive and well and making his way back to Honduras, where he's apparently from.
Jennifer Podkul, director of policy for Kids In Need of Defense, said she has spent time at the Casa Padre facility and finds it hard to believe the teenager could just walk away.
"There is barbed wire, there are armed guards, it is not an open facility," Podkul told ABC News. "A child does not have the option of walking out the front door. And their communication with the outside world is severely restricted. I don't know how a child would plan that kind of escape."
Eller said there is no barbed wire and security is posted outside the facility to protect children and staff, not to keep children inside.
"We don't have armed guards," Eller said. "We have security monitors inside the facility. However, due to the increased visibility of Casa Padre, we are utilizing off-duty sheriff's deputies, who are licensed peace officers to provide security on the outside of the building."
Southwest Key's Casa Padre location is the largest shelter for undocumented children in the country and has become a flash point in the debate over President Donald Trump's "zero-tolerance" policy that separated children from parents caught attempting to cross the border illegally. Last week, the president signed an executive order ending the family separation policy.
The Brownsville facility houses about 1,500 migrant boys ages 10 to 17.
ABC News' Tom Llamas visited the clean and well-staffed facility last week. Several activities to keep the children busy took place during his tour.
Austin-based Southwest Key operates at least 16 residential facilities across Texas, with 10 more in Arizona and California. About 10 percent of the children currently in its care were separated from their parents under Trump's "zero-tolerance" policy, according to the company.
Public records indicate the company employs around 4,500 people, and the company says it has served more than 23,000 children over the past two years.
Southwest Key has been awarded $458.7 million in federal money to care for kids detained at the border so far this year, including children separated from their parents and minors attempting to cross the border alone.