The question from Evans Davies came after Sacks delivered the Thought for the Day on the BBC Today program on Radio 4.
"I think it's got to do with Iran, actually," Sacks responded, adding a call for peace prayers when he was told he was talking into a live microphone.
The BBC said Davies was not trying to put Sacks on the spot.
"Evan likes to be spontaneous with guests but he accepts that in this case it was inappropriate and he has apologized to Lord Sacks," a spokesman said. "The BBC would reiterate that apology."