On Tuesday, the DUP's Trevor Clarke admitted he did not know heterosexual people could contract HIV until a charity explained the facts to him.
Sir Elton was appearing on the Victoria Derbyshire programme on Friday.
She asked him about his charity foundation and a survey that showed many myths about Aids and HIV endure in the UK.
"I'm not surprised," Sir Elton replied. "A Northern Ireland politician said the other day he didn't know that heterosexual people could get Aids, or HIV.
"So, it's like: 'What planet are you living on?'"
Sir Elton did not refer to Mr Clarke by name.
Mr Clarke made the admission in a Northern Ireland Assembly debate calling for a new HIV awareness campaign.
He was later accused of "unconscious homophobia" by Foyle MLA Eamonn McCann.
This was after Mr Clarke claimed an amendment by Mr McCann, stressing the disproportionate impact on gay and bisexual men, added to "stigma" on HIV.
Addressing the assembly, Mr Clarke said: "When I came here in 2007, I would have dismissed the possibility that I would speak about HIV today, because I was one of those who did not understand the stigma attached to it."
The DUP MLA added: "I have to put on record my thanks to Jacquie Richardson from Positive Life. Meeting her for the first time was a turning point for me, having been ignorant of the fact that the disease also affects heterosexual people.
"For that reason, I have no difficulty supporting what the motion calls for," he said. "The work that Positive Life did in changing my opinion - not only my opinion but that of many others - helped to remove the stigma."
Sir Elton John has criticised comments about Aids by a Northern Irish politician.