On Wednesday, immigrants rights groups filed a complaint against the U.S. Department of Homeland Security alleging the sexual and physical abuse of 116 unaccompanied migrant children at the border by U.S. Customs and Border Protection agents.

"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.

The 25-page-long complaint was filed by the American Civil Liberties Union, Esperanza Immigrants Rights Project, National Immigrant Justice Center, Americans for Immigrant Justice, and Florence Immigrant and Refugee Rights Project, according to CNN. The complaint alleges that for years, abuse of children from the ages of five to 17, who are mostly from Central America and Mexico, has taken place in Texas and Arizona, Reuters reports. According to Fox News Latino, the information came from interviews conducted from March to May, and most of the abuse occurred in the past year.

"After completing a perilous journey into the United States, many are subjected to various forms of abuse, harassment and other harms at the hands of the Border Patrol," the complaint says. "Children consistently reported being held in unsanitary, overcrowded and freezing cold cells."

According to CNN, other examples of alleged abuse include dozens of children sharing cells with one toilet and 70 percent of children being held longer than the 72-hour detention period. Four out of five children said they did not get enough water.

More examples of abuse include a 13-year-old boy allegedly being sexually molested and threatened with a metal rod, a 14-year-old girl getting her asthma inhaler taken away and a 14-year-old boy being deprived of sleep, Fox News Latino reports.

Despite the recent influx of unaccompanied minors crossing the border, mostly from Central America, illegally, Customs and Border Protection says abuse is not accepted.

"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," Michael Friel, a Customs and Border protection spokesman, told Reuters.

The National Border Patrol Council, which represents about 17,000 staff members according to Reuters, also said that steps are taken to prevent abuse.

"The vast majority of these allegations turn out to be unfounded or a thinly veiled attempt to delay prosecution," Shawn Moran, National Border Patrol Council vice president, told Reuters.

DHS has yet to reveal whether or not they are investigating the allegations, CNN reports.

According to data from Border Patrol, the number of children illegally immigrating from El Salvador, Guatemala and Honduras without adults has increased over 1,000 percent. In fiscal year 2009, 3,304 children from those countries were caught at the border. This year, that number has already exceeded 48,000.

Follow Scharon Harding on Twitter: @ScharHar.