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The Biden administration over the weekend shuttered a Houston warehouse that housed unaccompanied migrant children following allegations that the nonprofit organization running the site failed to provide adequate living conditions for hundreds of young girls, multiple sources familiar with the matter told ABC News.

The Department of Health and Human Services (HHS) opened the warehouse early this month in response to the surge of migrants arriving at the southern border.

Exclusive video shot by ABC News showed buses removing more than 100 girls from the emergency intake center on Saturday. Until its closure, the facility had been run by a Houston-based nonprofit with no prior experience housing unaccompanied migrant children.

Sources familiar with the facility’s operation said the girls housed there, aged 13-17, were at times instructed to use plastic bags for toilets because there were not enough staff members to accompany them to restrooms. A spokesperson for the nonprofit would neither confirm nor deny these allegations to ABC News.

A lack of outdoor space meant girls spent most of the day on makeshift cots surrounded by boxes intended to offer some semblance of privacy, according to the sources. The facility also suffered from overcrowding and failed to comply with pandemic-related distancing measures, the sources said.

Cesar Espinoza, the executive director of migrant civil rights organization FIEL, toured the facility in recent weeks as part of his work to ensure humane treatment for migrants, and said he saw “desperation” in the girls’ faces that was “unbearable and incredible.”

Espinoza said the warehouse space was “filled just with cots, where the girls were not allowed to get up, unless it was to shower, or to use the restroom. Even their meals were delivered to their cots.”

“[The girls] were more treated like merchandise rather than treated as human beings, as people who just went through a very traumatic experience,” Espinosa said. “I would not allow my 15-year-old sister to go and volunteer in a place like this because I don’t know what she’s going to see.”

Over the weekend, HHS announced it would relocate the nearly 500 girls to other facilities in the area, or to family members or sponsors.

“The children being transferred are being moved to ensure continuity of care under conditions that meet our strict standards of care,” an HHS spokesperson told ABC News.

A White House spokesperson told ABC News that the site was closed because it “did not meet the Biden administration’s very high standard for child welfare.”

Located near the George H.W. Bush International Airport, the migrant care facility was intended as an emergency stopgap measure to shelter the influx of unaccompanied minors entering the U.S.

The National Association of Christian Churches (NACC), a Houston-based organization with its roots in disaster relief, was awarded a $4 million contract to operate the warehouse despite having no record of caring for unaccompanied migrants.

In a statement to ABC News on Sunday, Dean Hoover, a spokesperson for NACC, sought to redirect blame toward the Biden administration — who NACC claimed had control over the site after bringing in its own subcontractors.

“NACC officials were personally requested by HHS Secretary [Xavier] Becerra and President Biden to open the doors of their large Houston facility to refugee children on an emergency basis,” Hoover said. “It is deeply hurtful and unfair to the folks at NACC that anyone would now think of criticizing them when all they were trying to do is be good Samaritans and help the HHS help these children.”

In recent interviews with the Houston Chronicle, Jose Ortega, NACC’s founder and president, claimed that his organization had not sought out this work — but rather that Becerra had personally “begged” him to accept the contract and house the children.

“I’m a humble pastor that was thrown into this mess without asking for it,” Ortega told the newspaper. “We were not looking for a contract, we were not applying for a contract for us to make money — this was thrown on us.”

Ortega also pinned the deterioration of his group’s facility on the government’s failure to provide funds.

A spokesperson for HHS, which oversees the Office of Refugee Resettlement, told the Houston Chronicle that NACC was vetted following standard procedures.

But advocates like Espinoza say the administration needs to better explain why it signed a contract with NACC.

“What was the process? Why was this center chosen?” Espinoza said to ABC News. “There’s many other spaces here in Houston that could have been chosen, that would have stepped up to the plate, who had the experience of running shelters or who have the experience of working with children in this space.”

Neither the White House nor HHS would say how NACC was selected despite having no prior experience housing migrant children or running a migrant holding center.

A steadily rising flow of migrants trekking north from Central America has sparked a humanitarian crisis near the U.S.-Mexico border, posing an early challenge to the Biden administration.

On Saturday, Biden acknowledged that the situation at the border does, indeed, amount to a crisis — a characterization his administration had previously refrained from using.

ABC News’ Katherine Faulders, Benjamin Siegel, Quinn Owen and Alex Hosenball contributed to this report.