At the start of his three-nation African tour in the Senegalese capital, Dakar, on 28 June, Mr Obama said gays deserved equal rights.
Homosexual acts are illegal in 38 African nations.
Speaking in Nairobi the next day, Njue, president of the Kenyan bishops' conference, said Obama, whose father was Kenyan, should forget the decriminalisation of homosexuality.
"Let him forget and forget and forget ... I think we need to act according to our own traditions and our faiths," said Njue. "Those people who have already ruined their society ... let them not become our teachers to tell us where to go."