Speaking to PinkNews.co.uk about an upcoming documentary, the gay Radio 1 presenter told how he feared for his own safety in the country.
Mills met anti-gay MP David Bahati as part of filming for ‘The World’s Worst Place to be Gay?’.
When the presenter said he was gay, Bahati became enraged and the film crew fled.
Later, they heard that Bahati had sent armed police to a hotel he thought they were staying at.
“I was really frightened,” Mills said. “It’s just something that you wouldn’t think would happen. It was a real shock to the system and we were told to lie low.”
He said: “I wasn’t aware before I went about what was going on in Uganda.
“I met gay people in safe houses because they had to flee their homes. The newspapers print their names, their photos, even what car they drive. These people are just hounded.
“It’s so bizarre that somewhere just seven hours away by plane can be so different.”
During filming, Mills met victims of homophobia and the pastors preaching against homosexuality.
“All the gay people we met had a story about how they had been tormented or attacked,” he said.
“There was a guy we saw in hospital, he had AIDS and was very ill. But because they knew he was gay, he wasn’t getting the right treatment. He’s dead now.
“Then there was a girl called Stosh, who had to go into hiding after her face was plastered across the newspapers.
“It’s all very well reading about these things but when you actually go to Uganda, you realise how bad things are. It was a lot worse than I expected.”
Gay people in Uganda have “an air of optimism”, he said. “But they’re faced with every pastor, every teacher in every school, saying the same thing.
“They think things will change but it’s going to take a long time.”
When asked how attitudes could change, Mills said: “I don’t really know. The West has been quite vocal and President Obama publicly denounced Uganda but [the preachers] still say homosexuality is un-African, that it is against the family.
“They think it was brought in by the West.”
Many of those he met had been accused of “promoting” homosexuality and “recruiting” children.
He said: “The pastors claim that gay people go into schools and offer children money but when you talk to the schools, they say it hasn’t happened. There’s no evidence for it.”
The film crew also saw first-hand the influence Western preachers have on anti-gay sentiment in Uganda.
“It’s all wrapped up in Christianity and evangelicalism,” Mills said. “And Americans come over to preach. We went to a sermon and saw a guy from Atlanta preaching gay hate.”
He added: “I went to Uganda with the aim of making a fair and balanced film but in two weeks, we couldn’t find any [non-gay] person saying that homosexuality was okay.”
‘The World’s Worst Place to be Gay?’ will be shown on BBC Three at 9pm on Monday February 14th.