Al-Qaeda regularly posts audio and video tapes on the internet
Al-Qaeda's deputy leader, Ayman al-Zawahiri, has blamed Iran for spreading the theory that Israel was behind the 11 September 2001 attacks.
In an audio tape posted on the internet, Zawahiri insisted al-Qaeda had carried out the attacks on the US.
He accused Iran, and its Hezbollah allies, of trying to discredit Osama Bin Laden's network.
Correspondents say the comments underline al-Qaeda's increasing public hostility towards Iran.
In a two-hour audiotape posted on an Islamist website, Osama Bin Laden's chief deputy responded to questions posted by al-Qaeda sympathisers.
In response to a question about persistent rumours in the Middle East that Israel was involved in the 9/11 attacks, Zawahiri said the rumour had begun on the Hezbollah television station, Al-Manar.
"The purpose of this lie is clear - [to suggest] that there are no heroes among the Sunnis who can hurt America as no-one else did in history, he said.
"Iranian media snapped up this lie and repeated it."
Zawahiri went on to criticise Iran for co-operating with the US in its 2001 invasion of Afghanistan, that helped to oust the Taleban.
"Iran's aim here is also clear - to cover up its involvement with America in invading the homes of Muslims in Afghanistan and Iraq," he said.
This is the second verbal attack on Iran, a predominantly Shia Muslim country.
Earlier this month, in an audiotape marking the fifth anniversary of the fall of Iraq's leader Saddam Hussein, the al-Qaeda deputy accused Iran of planning to annexe southern Iraq and the eastern part of the Arabian peninsula.
BBC security correspondent Rob Watson says such messages appear designed to play on Sunni fears throughout the region of growing Iranian influence, and to present al-Qaeda as the best bulwark against Tehran.