Donnie McClurkin is among several gospel singers scheduled to raise money for the Illinois senator and Democratic presidential candidate at a concert in South Carolina this weekend.
McClurkin has drawn attention from gay rights activists for his views on homosexuality.
"I don't believe that it is the intention of God," McClurkin said Monday in a telephone interview. "Sexuality, everything is a matter of choice."
McClurkin said he does not believe in discriminating against homosexuals. "What people do in their bedrooms and who they are as human beings are two different things," he said.
In a statement, Obama said he believes gays and lesbians are "our brothers and sisters" and should be afforded the same respect, dignity and rights granted all other citizens.
"I have consistently spoken directly to African-American religious leaders about the need to overcome the homophobia that persists in some parts our community so that we can confront issues like HIV/AIDS and broaden the reach of equal rights in this country," Obama said. "I strongly believe that African Americans and the LGBT community must stand together in the fight for equal rights. And so I strongly disagree with Reverend McClurkin's views and will continue to fight for these rights as president of the United States to ensure that America is a country that spreads tolerance instead of division."
The statement did not say whether McClurkin will still perform on the tour.
"We strongly urge Obama to part ways with this divisive preacher who is clearly singing a different tune than the stated message of the campaign," Wayne Besen, executive director of Truth Wins Out, said in a statement.
At a forum on gay issues in August, Obama argued that civil unions for same-sex couples wouldn't be a "lesser thing" than marriage. Obama belongs to the United Church of Christ, which supports gay marriage, but Obama has yet to go that far.
In a telephone interview Monday, Besen said he admired Obama, but wasn't ready to endorse him, especially considering McClurkin taking part in the campaign's "Embrace the Change" concert tour.
"I think he'd be a great president. But I think it's going to drive away support from people who are on the fence such as myself," Besen said.
McClurkin is a Grammy Award winner who performed at the Republican National Convention in 2004. He told AP Radio in an interview that September that he was "once involved with those desires and those thoughts," which he attributed to being raped at 8 and 13.
"That's what thrust me into it, and then God delivered me from that and gave me back who I really am and my true purpose," McClurkin said.