A bus leaves the entrance of the U. S. Border Patrol facility on Saturday, June 7, 2014 in Nogales, Ariz. Arizona officials said they are rushing federal supplies to this makeshift holding center in the southern part of the state that's housing hundreds of migrant children and is running low on the basics.

AP Photo/Brian Skoloff

A group of five organizations today filed a complaint to the Department of Homeland Security on behalf of 116 unaccompanied immigrant children who they said experienced abuse and mistreatment while in custody.

"We are coming forward now with more than 100 complaints but we believe thousands of children have be subjected to these conditions," said Joseph Anderson, director of litigation with Americans for Immigrant Justice.

"Although the surge of unaccompanied exacerbates this problem," he said during a telephone conference with reporters, "it predates this problem."

The organizations, which includes the American Civil Liberties Union Border Litigation Project and the Arizona-based Florence Immigrant and Refugee Rights Project, urged the federal government “to conduct a prompt and thorough investigation into each of these allegations,” which they say are part of a systemic abuse of unaccompanied children by Customs and Border Protection.

The complaint includes cases of children interviewed from March through May 2014, in which:

• More than 80 percent of the 116 children reported inadequate food and water by CBP officials;

• More than half reported experiencing some form of verbal abuse;

• One in four reported physical abuse ranging from sexual assault to punching, kicking and use of stress positions as punishment;

• One in three reported CBP confiscated and did not return money and/or belongings and about 15 percent reported being forcibly separated from family members.

In an email statement, CBP said it strives to protect unaccompanied children with special procedures and safeguards.

"CBP is ensuring nutritional and hygienic needs are met; that children are provided meals regularly and have access to drinks and snacks throughout the day; that facilities include toilets; that they receive constant agent supervision; that children who exhibit signs of illness or disease are given proper medical care," the agency said. "Mistreatment or misconduct is not tolerated."

The complaint comes as the federal government grapples with a surge of children crossing the border illegally without parent or guardians.

"In the face of overwhelming numbers of unaccompanied children crossing the border in South Texas, U.S. Border Patrol agents have taken extraordinary measures to care for these children while in custody and to maintain security in overcrowded facilities," agency officials said.

Since last week, CBP has been flying children over to be processed in Arizona. CBP reopened a warehouse that had been refurbished as a processing center to temporarily hold Mexican nationals when the Tucson sector was going through its own surge of border crossers.

Over the weekend it brought in showers, televisions, laundry machines, and other amenities, but consular officials from Central America have said it is not a detention place adequate to hold children, especially for long periods of time.

The federal government is supposed to transfer children into the custody of the Office of Refugee Resettlement, under the Health and Human Services Department, within 72 hours.

But due to more than 47,000 children having been apprehended so far this fiscal year, the agency has run out bed space.

About 70 percent of the 116 children and youth included in the complaint said they were detained for more than 72 hours.

"CBP does everything within its power to process these children as quickly as possible in order to transfer them to the Department of Health and Human Services within 72 hours absent exceptional circumstances, as required by law," the agency's statement read.