Chapter Four Uganda documented several cases of men suspected of being homosexual having intrusive physical examinations.
Homosexual acts are illegal in Uganda and there are plans to introduce new harsher legislation.
Uganda’s internal affairs minister said the allegations were not true but his office would look at the findings.
Aronda Nyakairima told the BBC that the Ugandan government did not discriminate against anyone.
Where is is legal to be gay?
The 27-page report entitled Where Do We Go for Justice? said officers routinely refused to look into cases reported by gay men and lesbians.
It found several instances when the police instead turned against them because of their sexuality, charging them with crimes such as indecent exposure, sodomy and having sex against the order of nature.
They were harassed into signing false and self-incriminating statements and some of the 21 people interviewed by researchers also talked of being beaten by the police or prison wardens.
Some said they were forced to have their rectums and genitals examined…story continues below…