Bin Laden made the charge in an audio recording posted on an Islamist Web site. He linked the pope to Danish cartoons published two years ago. A cartoon that showed Mohammed with a bomb in his turban was reprinted late last year after Danish police found an alleged conspiracy to kill the cartoonist.
Federico Lombardi, a Vatican spokesman, said that Benedict spoke against the cartoons when they were originally published, The Times of London reported.
"It is natural to think that he would lump the Vatican and the pope together with all his perceived enemies," Lombardi said. "But this is not correct."
The pope angered many Muslims in 2006 with a speech at Regensburg University in Germany that appeared to suggest Islam is an intrinsically violent religion. Since then, Benedict has prayed in the Blue Mosque in Istanbul and is to address the first Catholic-Muslim Forum in November.