"Rape, physical intimidation, sexual harassment, and even so-called 'virginity tests' have taken place in countries throughout the region," she said in a statement.
"Kadhafi's security forces and other groups in the region are trying to divide the people by using violence against women and rape as tools of war, and the United States condemns this in the strongest possible terms."
International Criminal Court prosecutor Luis Moreno-Ocampo said last week that there was evidence the Libyan authorities bought "Viagra-type" medicines and gave them to troops as part of an official rape policy.
"Recently, the International Criminal Court has taken note of the appalling evidence that rape in Libya is widespread and systematically employed," Clinton said.
"A thorough investigation of this matter is needed to bring perpetrators to justice."
Clinton mentioned Iman al-Obeidi, whose accusations of rape against soldiers loyal to Kadhafi garnered worldwide attention when she stormed into the Rixos hotel in Tripoli -- where many Western journalists were based -- and threw open her coat to reveal scars and bruises on her body.
"Since Iman al-Obeidi bravely burst into a hotel in Tripoli on March 26 to reveal that Kadhafi's security forces raped her, other brave women have come forward to tell of the horrible brutality they have experienced," she said.
"It is an affront to all people who are yearning to live in a society free from violence with respect for basic human rights. We urge all governments to conduct immediate, transparent investigations into these allegations, and to hold accountable those found responsible."
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