Rupert, 53, told the UK's Sunday Times Magazine that he agrees with his 77-year-old mother's opinion that "children need a father and a mother".
"I can't think of anything worse than being brought up by two gay dads," Rupert said in the interview.
"Some people might not agree with that. Fine! That's just my opinion."
Madonna's former best gay buddy elaborated further on his sentiments.
"I'm not speaking on behalf of the gay community. In fact, I don't feel like I'm part of any 'community'," Rupert said.
"The only community I belong to is humanity and we've got too many children on the planet, so it's good not to have more."
Rupert made the comments with reference to his mother meeting his current boyfriend.
LGBT groups have expressed their disappointment in Rupert for his inflammatory remarks.
"Rupert should get out a little bit more to see the facts for himself. There is absolutely no evidence that the kids of gay parents suffer in the way they are being brought up or in how they develop," said Ben Summerskill, the chief executive of LGBT rights group Stonewall.
It's not the first time Rupert has angered the gay community. Rupert, who came out as gay in 1989, advised young gay actors to stay in the closet about their sexuality if they wanted to get work.
"It just doesn't work and you're going to hit a brick wall at some point," he said in a 2009 interview.
In the latest Sunday Times interview, Rupert's mother, Sara McLean Everett, said she wished Rupert was straight and married to a woman.
"I'd like him to have children. He's so good with children. He'd make a wonderful father," she said.
"But I also think a child needs a mummy and a daddy. I've told him that and he takes it very well. He doesn't get angry with me. He just smiles."
Maybe Rupert needs a bit of publicity for his upcoming second tell-all memoir. Seriously, how much can there be to tell all about?