(CNN) -- Threats of violence. Sexual abuse. Strip searches. Dirty conditions. Young mothers whose children became sick.
These are among the reported abuses of 116 minors by agents from U.S. Customs and Border Protection, according to a complaint filed Wednesday by the American Civil Liberties Union and four immigrant-rights groups.
The groups say in their complaint that the incidents have been occurring for years and called for an investigation and improved federal policies toward young undocumented immigrants.
"Given these longstanding problems, and in light of the rising number of unaccompanied children seeking relief from dangerous conditions in their home countries, the need for broad and lasting agency reforms is clear," the complaint says.
A spokesman for Customs and Border Protection said the agency has taken "extraordinary measures" to look after the children, some of whom are new parents.
Michael Friel wrote in an e-mail that children get regular meals and drinks, constant monitoring, and those who appear sick get medical care.
"Mistreatment or misconduct is not tolerated," he added.
The crisis of unaccompanied minors from countries such as El Salvador, Guatemala and Honduras is growing.
Because the children are not from countries that border the United States, federal law prohibits them from being immediately deported. Instead, after three days they are turned over to the Department of Health and Human Services.
But the ACLU and the other organizations say children have too often reported incidents of abuse, freezing cold cells and rooms where dozens of people are jammed in with access to only one toilet. About 70% said they were held past the 72-hour detention period.
Four out of five described a lack of water and enough food, according to the complaint, addressed to the Department of Homeland Security's Office for Civil Rights and Civil Liberties and the department's inspector general. Americans for Immigrant Justice, the Esperanza Immigrant Rights Project, the Florence Immigrant and Refugee Rights Project and the National Immigrant Justice Center also joined the complaint.
The children were between the ages of 5 and 17 when the incidents allegedly occurred.
DHS wouldn't comment on whether it was investigating the allegations.
Chris Cabrera, a leader of a chapter of the National Border Patrol Council, a labor union representing U.S. Border Patrol agents, estimated that more than 60,000 unaccompanied juveniles will cross the Mexican border with the United States in 2014 and that the numbers will rise from there.
Many of the youths turn themselves in to the Border Patrol.
"They know that once they get to the station, we are going to give them paperwork and we are going to set them free into the United States," Cabrera said.
The numbers are overwhelming American facilities, particularly in Texas.
On Wednesday, Homeland Security chief Jeh Johnson told a Senate committee that he recently visited the border.
He also told Judiciary Committee that the U.S. would open three new facilities to house the children and would pull scores of agents from their duties watching the border so they could watch the youths.
CNN's Mary Kay Mallonee contributed to this story.