"A lot of LGBTI people found it comfortable to go there for anti-retroviral treatment," he said.
Patrick Onyango, a spokesman for Ugandan police, denied the raid, saying a man pretending to represent the police threatened workers at the project. He said that authorities were now looking for the man, after police in his jurisdiction briefly arrested him and then freed him.
Daniel Travis, a spokesman for the U.S. Embassy in Kampala, declined to comment.
Uganda's president in February enacted a new measure that allows up to life imprisonment for those convicted of engaging in gay sex and sets a seven-year jail term for the offense of "attempted homosexuality." Despite criticism from the U.S. and other Western countries that say the law is draconian and should be repealed, it has wide popularity among Ugandans.
On Monday it became the first legislation in Uganda to be publicly celebrated in a rally attended by Ugandan President Yoweri Museveni, who told a raucous crowd that he was "mobilizing" to fight Western gays he accuses of promoting homosexuality in Africa. At that rally, attended by thousands of Ugandans, Museveni said gays deserve to be punished severely because homosexuality is "criminal and it is co cruel."
The U.S., the World Bank and some European countries have cut, delayed or reviewed development assistance to Uganda since the bill was enacted, action that some Ugandan government officials have described as blackmail.
Ugandan gay leaders say many homosexuals have had to flee their old homes in the weeks since the measure was enacted, apparently to escape angry mobs, and some are reported to have been evicted by landlords who discovered they were gay.
Mugisha, the gay leader, said he recommended the project's clinic to many homosexuals because workers there were "without bias."
The project says on its website that its objectives include monitoring trends in the HIV epidemic in Uganda and conducting HIV vaccine trials. The project opened in 2002 and has since expanded its activities to include HIV prevention, care and treatment. Through the U.S. President's Emergency Fund for AIDS Relief, or PEPFAR, the project has been running HIV programs across Uganda.
About 1.5 million Ugandans are infected with HIV, according to UNAIDS, the United Nations program on HIV and AIDS.
Maria Burnett, a Uganda researcher with Human Rights Watch, warned Friday that the anti-gay measure makes it hard for homosexuals to access confidential medical services.
"The Ministry of Health keeps reassuring everyone that the (anti-gay) law will not result in discrimination and stigma in access to health care services and research but yesterday's events clearly contradict that," she said.