Lior Shlein has apologised for the skit from his late-night talk show
Israeli Prime Minister Ehud Olmert has issued an official apology after a comedy skit on a TV programme caused outrage among the Christian community.
Private broadcaster Channel 10 aired a show last week depicting the Virgin Mary as a pregnant teenager and Jesus as being too fat to walk on water.
The Vatican issued a statement denouncing the broadcast as an "offensive act of intolerance".
The row has strained already tense ties between the Vatican and Israel.
"I condemn the comments made during this televised programme," Mr Olmert said at the weekly cabinet meeting on Sunday.
"I regret these comments against Christians, especially since they target the Christian community in Israel."
In the popular late-night talk show, Israeli comedian Lior Shlein railed against Christian beliefs - that Mary was a virgin and that Jesus walked on water - saying he was doing so as a "lesson" to Christians who deny the Holocaust.
It was a reference to Pope Benedict XVI's recent decision to lift the excommunication of British bishop Richard Williamson, who has said that no Jews had been gassed during the Holocaust and that only 200,000 or 300,000 Jews had been killed.
The move sparked protests from Jewish community leaders and Israeli authorities.
Following the Channel 10 broadcast, the Vatican said the show had ridiculed Mary and Jesus "with blasphemous words and images" that amounted to a "vulgar and offensive act of intolerance".
In the show, Mary is said to have become pregnant at 15, thanks to a schoolmate.
It said Jesus could never have walked on water because "he was so fat he was ashamed to leave the house, let alone go to the Sea of Galilee with a bathing suit".
Mr Shlein, who hosts Channel 10's nightly Tonight Show, has apologised for the remarks. The station also assured the Israeli foreign ministry that the segment would not be shown again.
The latest row comes ahead of a planned visit by the Pope to the Holy Land in May.