McAleenan struggled to mesh with the Trump administration.
Activists said the acting secretary's appearance at a law school conference would have given the Trump administration a "platform to spread hatred."
Kevin McAleenan expressed frustration to The Washington Post about his inability to control the department's approach "in an increasingly polarized time."
U.S. immigration officers arrested 680 people just a few days after a gunman in El Paso, Texas, targeted Mexicans in a mass shooting.
Communities scrambled to find beds and food for children suddenly left alone at schools and day care after their parents were rounded up in mass raids.
Freshman lawmaker Alexandria Ocasio-Cortez asked acting DHS Secretary Kevin McAleenan if Trump's policies had contributed to a "dehumanizing culture."
Kevin McAleenan told ABC's "This Week" that the slew of reports on unsafe and unsanitary conditions at Border Patrol facilities are unsubstantiated.
"Our transportation is based on operational necessity," said Kevin McAleenan, acting secretary of the Department of Homeland Security.
The acting DHS chief said he regretted that the policy led to a loss in faith, but didn't mention the thousands of children separated from their parents.
The Department of Homeland Security denied the report, which CNN sourced to two senior administration officials.
President Donald Trump announced that U.S. Customs and Border Protection Commissioner Kevin McAleenan would take over for Nielsen on an acting basis.
The U.S. Customs and Border Protection commissioner will replace Kirstjen Nielsen as Department of Homeland Security secretary.
Nielsen and Trump had reportedly clashed over enforcement of the nation's immigration policies.
“If I was the head of DHS, I would ask him to step down,” said U.S. Rep. Joaquín Castro of Texas.
“It’s standard law enforcement issue," Kevin McAleenan told CNN's Chris Cuomo.