"I didn't think it is possible that Osama sitting up there in the mountains could do it," Musharraf told The New Yorker magazine in the issue appearing on newsstands Monday.
Speaking of bin Laden, Musharraf said in the interview: "He was perhaps the sponsor, the financier, the motivating force. But those who executed it were much more modern.
"They knew the U.S., they knew aviation. I don't think he has the intelligence or the minute planning. The planner was someone else."
Musharraf does not say who he thinks was behind the attacks.
The United States blames bin Laden and his al Qaeda network, which had a foothold in Afghanistan prior to Sept. 11, for the attacks.
Pakistan was the chief backer of the Afghan Taliban before Sept. 11, after which Musharraf switched sides and joined the U.S.-led war against terrorism.