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The groups say that the number of victims of "sexual cleansing" is growing on a daily basis.
"In the past three months, more than 30 gays have been executed in Baghdad. The bodies have been found tortured, mutilated - sometimes with signs of rape," said Mustafa Salim, spokesman for the Rainbow for Life Organisation (RLO), a Baghdad-based gay rights NGO.
"Notes were found near some of the bodies with messages saying that this is going to be the fate for any Muslim who denies the Islamic religion," Salim added.
RLO was set up in 2005, and Salim claims that since then they have recorded more than 230 cases of abuses against gays and lesbians, including more than 64 deaths - with the last three months being the most bloody.
"The gay community continues to be subjected to systematic terror by Shia militias, especially the Mahdy Army controlled by the religious leader Muqtada al-Sadr. The government of Iraq is refusing to offer protection," he added.
In an interview, one member of the Mahdy Army, Ali Hassany, said that the militia will target Iraq's gays and lesbians.
"They deserve death. Those people are an embarrassment to our society. Killing such people is a job for their families, but if they cannot do so by their own hands, we will do it," Hassany said.
For security reasons, RLO has been keeping a very low profile. The whereabouts of its offices are unknown and it maintains clandestine contacts with victims and volunteers.
"Four of our volunteers have been killed since 2005 and many threats have been received, but we will not stop trying to help those people. They don't have anyone to help them and even the government considers them victims of common violence rather than victims of special targeting," Salim added.
The Iraqi Ministry of the Interior denies that the gay community is being singled out for violent attacks, and claims that the problem is general and related to sectarian violence.
"All Iraqis might be victims of violence. We cannot afford protection to a special group because the situation is delicate for all Iraqis and we cannot confirm that they have been targeted for being gays or lesbians," said Lt. Col. Hussein Jaboury from the ministry.
The United Nations Assistance Mission to Iraq (UNAMI) says that it agrees that gays and lesbians are being targeted by the militias.
"Armed Islamic groups and militias have been known to be particularly hostile towards homosexuals, frequently and openly engaging in violent campaigns against them," a report released in January by UNAMI said.
"There have been a number of assassinations of homosexuals in Iraq. We were also alerted to the existence of religious courts, supervised by religious scholars, where homosexuals allegedly would be 'tried', 'sentenced' to death and then executed," the report added.