Ayman al-Zawahiri said Musharraf helped the United States to topple the Taliban government in Afghanistan in the October 2001 invasion - support that killed thousands of innocents in the war-torn country.
During the broadcast on Sunday, the al-Qaida spokesman also claimed the Pakistani president was seeking to recognise Israel and send troops to Iraq in an attempt to gain full American approval.
"Musharraf ... is seeking to send Pakistani forces to Iraq so that they, rather than American soldiers, are killed and so that they kill Muslims in Iraq and enable America to control Muslim lands."
He also warned Pakistani army officers and soldiers the president would "hand you over to the Hindus and flee to enjoy his secret [bank] accounts" if India attacked their country.
Claiming no reward
Nor would Washington reward Musharraf for his services, according to al-Zawahiri.
Palestinian leader Yasir Arafat was "a living example" of what happens to "traitors", the speaker said.
"He gave Israel and America all that they asked for. But despite this, they are now incarcerating him in his office [in the West Bank town of Ram Allah] ... and lately decided to expel him."
"Musharraf ... is seeking to send Pakistani forces to Iraq so that they, rather than American soldiers, are killed and so that they kill Muslims in Iraq and enable America to control Muslim lands"
Al-Zawahiri also condemned Israeli Prime Minister Ariel Sharon’s recent visit to India, saying the agreements signed were “a drop in the ocean of the American-Jewish-Indian alliance against Muslims".
Although the CIA have described the recording as “probably authentic”, Aljazeera does not known when the tape was recorded.
But the remarks were replete with references to recent events such as Sharon's September visit to India and developments in Iraq and the Palestinian territories.
Al-Zawahiri also added al-Qaida’s Usama bin Ladin and Taliban’s Mulla Muhammad Umar were both alive.
The outburst against Musharraf is strikingly similar to attacks on the Pakistani leader in another al-Zawahiri audiotape broadcast on the eve of the second anniversary of 11 September.