The complaint was filed by five immigration rights groups on Wednesday on behalf of 113 children who reported experiencing abuse including sexual assaults and beatings in the last year.
It also alleges many of them were denied medical care, and adequate food and water. Most of the incidents allegedly took place in Texas and Arizona against children ranging between 5 and 17 years of age.
"Mistreatment or misconduct is not tolerated," a spokeswoman for US Customs and Border Protection said on Wednesday.
She added that the authorities go to extra lengths to ensure the safety of unaccompanied migrant children.
As many as 80,000 undocumented immigrant children, many travelling alone, are expected to be apprehended crossing the border into the US this year alone.
Joseph Anderson, the director of litigation for Americans for Immigrant Justice, said that one seven-year-old boy, developmentally disabled and unable to speak or walk was held for five days in Border Patrol custody.
Anderson added that the child was treated in a way that when he was handed over to the custody of Health and Human Services officials, he was rushed to a children's hospital where he had two emergency surgeries and stayed for some 40 days there.
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