Speaking before Clinton's seven-day trip to Africa, Johnnie Carson, the assistant secretary of state for African affairs, said: "The secretary is deeply concerned about the gender-based violence which is occurring in the eastern Congo."
The Congo Advocacy Coalition, a group of 88 humanitarian and human rights organisations, said on Monday that thousands of women and girls had been raped by either rebel fighters or government forces since the beginning of the year.
More than 600 people are believed to have been killed and, the United Nations estimates, at least 800,000 people have fled their homes due to the violence.
"The UN-backed offensive that was supposed to make life better for the people of eastern Congo is instead becoming a human tragedy," Marcel Stoessel, the head of Oxfam in DR Congo, said.
"Secretary Clinton needs to make it very clear that US support for the UN's efforts in Congo is not a blank cheque and that civilians should be protected."
DR Congo's abundant mineral riches, such as coltan which is used in the manufacture of mobile phones, have fuelled the violence in eastern areas of the country with rival militias competing for control.
The resource-rich area has also attracted Chinese companies, including the state-owned Sinohydro Corp and China Railway Engineering Corp, seeking to develop copper and cobalt deposits.
Clinton is on a seven-nation African tour which has so far taken her to Kenya, South Africa and Angola.
In Angola on Sunday, Clinton pressed the government to do more to fight corruption.
"Corruption is a problem everywhere and where it exists it undermines people's faith in democracy, it distorts governance," Clinton said at a news conference.
She praised Angola for publishing its oil revenues online and for working with US officials to increase transparency.
"Of course we raised this issue with the minister but I think it is only fair to add that Angola has begun taking steps to increase transparency," Clinton said after meeting Assuncao Afonso dos Anjos, Angola's foreign minister.
Angola, which rivals Nigeria as Africa's biggest oil producer, ranks 158th on Transparency International's 180-nation corruption index.
Clinton also urged the government to continue attempts to improve to build on successful legislative elections held in 2008 and pledged to boost trade ties with Luanda.
The visit was intended to reinforce Washington's presence in a country where it is increasingly competing for resources with China.
After meeting Assuncao Afonso dos Anjos, Angola's foreign minister, Clinton urged the government to build on successful legislative elections held in 2008.