Some Congolese soldiers were convicted of rape in May
Freedom From Torture said medical reports of 34 women showed many of them had been brutally gang-raped.
The women - who included traders and professionals aged between 18 and 62 - are seeking asylum in the UK.
Two Congolese human rights groups said, they had not received any reports of political rape in the country's prisons, although they said it might happen in secret detention centres.
In its report, Freedom From Torture said one woman was arrested and raped after organising a protest against sexual violence.
"There are some striking consistencies in the experiences of sexual violence and torture of the women in this report which strongly suggests that this horrific abuse is being routinely carried out in prisons in the DRC."
DR Congo is often dubbed the "rape capital of the world", with rights groups saying that rape and sexual violence has become a weapon of war since conflict broke out in the early 1990s in the east of the country.
In May, two soldiers were convicted of rape by a military court.
Freedom From Torture said women were raped by security force members to stop "women speaking out about politics, human rights and, in some cases, rape itself".
It says women were abused at several locations in the capital, Kinshasa 1,500 km (1,000 miles) from the conflict zones.
One woman, named as Faith in the report, said security agents raided her home in early 2013 after she organised an anti-rape protest in the province of Bas Congo, west of Kinshasa.
"One of them said: 'You are talking about rape, now we'll show you what rape means'. They raped my niece in front of us. Then they took me to prison," she is quoted as saying in the report.
"Now I know, because I have been there, that it is normal for women to be sexually abused in prison," she said.
"The soldiers and the prison guards, they don't see women as human beings, they don't see any value in women. I can't even remember how many times I was raped."
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