Several advocacy organizations filed a complaint with the Department of Homeland Security on Wednesday, claiming unaccompanied immigrant children are regularly mistreated while in Customs and Border Protection custody.

The complaint was filed on behalf of 116 children who were between the ages of five and 17. They allegedly suffered physical and sexual abuse; denial of food, water, and medical treatment; and were held by CBP far longer than legally allowed.

Joseph Anderson with Americans for Immigrant Justice said he thinks these conditions have existed for years.

"We believe thousands of children have been subject to these conditions, and that while the surge in the number of unaccompanied minors crossing the border exacerbates this problem, it's a preexisting problem and one that we feel the Department of Homeland Security has probably been aware of for some time," Anderson said.

Over the last eight months, Border Patrol agents have stopped more than 47,000 unaccompanied child migrants, almost double the number during the same time period last year.

"There is clearly a humanitarian crisis at the border, but the longstanding abuse of children by CBP is its own form of humanitarian crisis, one that's been allowed to persist for far too long," said James Lyall with the ACLU's Border Litigation Project. "This complaint is further proof that CBP is an agency in need of massive reform. This should be the final straw."

"I would categorically deny that Border Patrol agents are abusing illegal alien children that are crossing the border," said Shawn Moran. He's the vice president of the National Border Patrol Council, a union representing Border Patrol agents.

"In fact, I would say our agents go out of their way to make sure that illegal alien children that cross the border are well fed, well taken care of, and try to make it as comfortable as possible in (an) obviously difficult situation," Moran said.

CBP echoed the union's sentiment in a written statement, saying it "strives to protect unaccompanied children with special procedures and safeguards," and that "mistreatment or misconduct is not tolerated."

It continues that in light of the surge of unaccompanied children crossing into the United States, "Border Patrol agents have taken extraordinary measures to care for these children while in custody and to maintain security in overcrowded facilities."

Updated 6/11/2014 at 5:44 p.m.