"Immediate steps can and must be taken by governments and civil societies to stop these attacks on women and girls which increase their vulnerability to HIV," the group Women's Equity in Access to Care and Treatment said on Wednesday.
"There is an immediate need of women and girls there for protection from further rape and sexual torture, access to emergency medical services, including post-exposure prophylactic antiretrovirals, rape counselling as well as food and shelter."
Releasing its case studies on various African nations, it said systematic rape by warring groups would exacerbate seriously the AIDS pandemic that is already destroying the region.
Rape "is an engine of HIV infection", the group's executive director, Anne-Christine d'Adesky, told a news conference at the 15th International AIDS Conference in Bangkok.
More than 25 million people are living with HIV/AIDS in Africa, two-thirds of the world's total.
Rape was also widespread in Rwanda when it was embroiled in genocide in 1994. Of some 250,000 rape survivors, the group estimates that 67% are living with HIV.
And the number is expected to rise as more women come forward for HIV testing, d'Adesky said.
But while systematic rape in Rwanda seems to have stopped, the same cannot be said for Congo, northern Uganda and Greater Darfur in Sudan, where violence against women continues.
"The most recent human rights cases cite girls as young as three years old raped by knives, guns and sticks" in Congo, the group said.
"We talk about medicines, abstinence, the Global Fund at this conference, but when we are talking about women and children in conflict, these things mean nothing," said Beatrice Were, an activist based in Uganda.
"For women in war, their fight is to live, to get treatment. It's hard even to imagine how to get medication to these areas in the first place," said Were of Action Aid Uganda.
Were, who contracted HIV from her husband and who has two children, also told of the immense suffering faced by women who have been raped and who are living with HIV in Africa.
"Can you imagine the trauma of a woman who not only gets raped, but who contracts HIV because of that? She has to live with two stigmas, being raped and being HIV positive," Were said.
"And some even get pregnant. Can you imagine having to tell the child 'you are born out of wedlock, your mother is HIV positive and you may also be HIV positive'."