"We have no evidence that children went hungry," McAleenan told "This Week" Co-Anchor Martha Raddatz. "Police station cells are not a good place for children, as I've said dozens of times."
"We had an overflow situation with hundreds of children crossing every single day," he added.
McAleenan, who previously served as the head of U.S. Customs and Border Protection, said the agency has taken protective measures including building temporary processing facilities and ramping up medical staff. He also said the agency even overspent on such measures, hoping Congress would later provide the supplemental funds.
"If Illegal Immigrants are unhappy with the conditions in the quickly built or refitted detentions centers, just tell them not to come. All problems solved!" Trump wrote on Twitter this week.
For months, McAleenan has raised alarms about the potential for disastrous conditions on the southern border while maintaining his agency has upheld government standards for housing detainees, despite evidence to the contrary. He said on Sunday that the food and water at one facility in Clint, Texas, that has faced scrutiny were "adequate" and that migrants in holding centers had access to showers and clean living quarters.
"I'm not denying that there are challenging situations at the border, I've been the one talking about it the most," McAleenan said.
He said Homeland Security has reduced the number of children in their custody from 2,500 at the beginning of June to 350 children as of Saturday. McAleenan said the new funding to shelters run by Health and Human Services allowed them to move minors through the system more quickly, connecting them with case workers who will find approved sponsors to care for them upon release.
His remarks on Sunday cap another tumultuous week for Homeland Security as the agency has grappled with government watchdog reports of overcrowded and dangerous conditions at Border Patrol stations in the southwest.
Conditions were so severe at facilities in the Rio Grande Valley that one CBP manager described it to federal investigators as a "ticking time bomb" in the report made public this past week.
Government oversight authorities found that hundreds of children had been held in CBP custody well beyond the legal limit of 72 hours and most of them did not have access to showers or a change of clothes.