Immigration and Customs Enforcement's acting head, Mark Morgan, has been tapped to lead U.S. Customs and Border Protection, following John Sanders' resignation from the position, a government official told ABC News.
The change in leadership comes as CBP faces new round of scrutiny regarding the conditions at certain Border Protection facilities where children are being held and new allegations that children are being neglected while in the agency's custody at these locations.
Sanders made his announcement in an email to CBP employees, which was obtained by ABC News on Tuesday. His departure follows allegations made by independent inspectors who claimed migrant children were being kept at border stations with deplorable conditions, including a facility that one doctor compared to "torture facilities."
CBP officials, speaking on condition of anonymity, on Tuesday, denied allegations of mistreatment at Border Patrol facilities, but said an internal investigation was underway. Two other administration officials said Sanders' resignation was not tied to the recent allegations of neglect at one facility in Clint, Texas.
ABC News previously reported that physician Dolly Lucio Sevier, who was granted access to the largest CBP detention center in the country in McAllen, Texas, described the facility as having "extreme cold temperatures, lights on 24 hours a day, no adequate access to medical care, basic sanitation, water or adequate food."
In an earlier interview with ABC News, Lucio Sevier said the facility "felt worse than jail."
(MORE: Doctor compares conditions for unaccompanied children at immigrant holding centers to 'torture facilities')"It just felt, you know, lawless," she said. "I mean, imagine your own children there. I can't imagine my child being there and not being broken."
At a separate facility in Clint, Texas, lawyers said the conditions were just as bad.
Warren Binford is a law professor at Willamette University who interviewed children at the facility and said that there were infants and toddlers sleeping on concrete floors, as well as older children having to care for younger children -- a feat, he said, they were not equipped to do, ABC News has previously reported.
CBP officials told reporters on Tuesday that they had not seen evidence of neglect or abuse at the Clint facility and had returned 100 children to the center after being moved out.
When asked on the call if there was any concern about moving the children back to a facility that had allegations of mistreatment, one CBP official said they were "not concerned" because "a full investigation will be completed."
"And frankly, as I said earlier, I personally don't believe these allegations," the official told reporters.
But Lucio Sevier, told ABC News that she stands by her comments and that the U.S. Customs and Border Protection "cannot deny the deplorable conditions."
"I stand by what I said," she said.
That includes that the children in these holding facilities aren't getting access to soap, toothbrushes and showering only once every week to three weeks. The children were "dirty," she said. "I stand by everything."
Speaking on condition of anonymity, CBP officials told reporters that they were not short on items such as toothbrushes and that children were given snacks and juice on demand. They have refused news organizations access to the facilities, however, saying the officials there are too busy trying to process the children and find places for them at more long-term shelters.
Sanders has served as acting commissioner since April and is the chief operating officer of the agency. Sanders previously worked as the chief technology officer for the Transportation Security Administration, according to CBP, and has "more than 30 years of national security experience."
When he was tapped to serve as acting commissioner, acting Homeland Security Secretary Kevin McAleenan called Sanders "instrumental" to the agency.
"In addition to bringing greater focus on the agency's operational requirements, he has provided strategic direction and oversight to critical enterprise services and operations support functions across the agency. With John Sanders' leadership, CBP will continue to excel, remain ever vigilant, and accomplish the mission with steadfast resolve," McAleenan said at the time.
(MORE: Pelosi says Democrats to vote on emergency funding to help children at border detention centers)In his message, Sanders said he told acting DHS Secretary Kevin McAleenan his resignation was effective July 5.
"In that letter, I quoted a wise man who said to me, 'each man will judge their success by their own metrics,'" he wrote to employees. "Although I will leave it to you to determine whether I was successful, I can unequivocally say that helping support the amazing men and women of CBP has been the most fulfilling and satisfying opportunity of my career."
He later added, "Don't underestimate the power of momentum as you continue to tackle some of this country's most difficult challenges."
Morgan previously served chief of Border Patrol with CBP before he began his role with ICE.
In an interview earlier this year with Fox News' Tucker Carlson, Morgan said that he had been to detention facilities "where I've walked up to these individuals that are so-called minors, 17 or under, and I've looked them, and I've looked at their eyes, Tucker, and I've said, 'That is a soon-to-be MS-13 gang member.' It's unequivocal."
ABC News' Jim Avila, Serena Marshall, Lana Zak and Jennifer Metz contributed to this story.