The three-day meeting organised by Eastern Horn Human Rights Defender’s project was specifically for the gay community in the region.
A statement by a coalition of rights groups, including Freedom House and Amnesty International, dubbed the raid "arbitrary and an illegitimate infringement on freedom of association and assembly".
The meeting has since been called off.
Julian Pepe Onzima the programme director and acting advocacy officer for sexual minorities in Uganda said the meeting was on monitoring, documentation and reporting of human rights abuses in Uganda and the region.
“People are shaken, there is no way anyone is going to concentrate when they are in fear, the meeting cannot go forward,” he told RFI. “ Every part of the hotel where there was an outlet was blocked by police so no-one could move including people of the media. Rooms were searched , people had to be evacuated from the hotel to a safer place.
Five participants were briefly detained and later released without any charges.
They included an intern, a legal officer and researcher from the Eastern Horn Human Rights Defenders project, an activist from Freedom House and another from Gay Kenya Trust organisation.
““The minister of ethics is not going to intimidate me into silence and we shall continue to talk about these issues," Pepe said. "It’s total abuse of power that the minister is carrying on his ambition to clamp down our existence as part of society in Uganda. We are going to continue pursuing justice through the courts of law.”
Homosexuality is illegal in Uganda and sexual minorities have been hit several times by government officials.
In 2009 Member of Parliament David Bahati tabled an anti-homosexuality bill in parliament.
The bill seeks to criminalise same-sex relationships. The bill, which is currently shelved in parliament, proposes stiff penalties for homosexuals from 14 years to life in jail.
“We are worried, since the bishops came out and supported the bill to be passed, because its content is contrary to the constitution," Pepe said. "It’s really sad that, instead of the country having laws that protect its citizens, it's actually creating laws that infringe on their rights as citizens of Uganda and make them live in fear.”