The Muse frontman was quoted in 2006 as saying that that there was "massive evidence" to suggest that US authorities either allowed the attacks to occur or "deliberately" made them happen.
"There was a document called 'Project for the New America Century'... which clearly says, 'We need a Pearl Harbour-level event so we can have an excuse to invade the Middle East'," he said at the time.
"I don't believe that any more, although there are lots of questions to be answered," Bellamy told Metro.
"I still read a lot about political history, the influence of corporations and the military, but I make sure I'm reading from credible sources. I think my political views are a bit more nuanced now."
Of Muse's plans for their upcoming arena tour, Bellamy said: "We have a symbolic upside-down pyramid suspended over us as we play. It will screen videos and images that relate to the songs.
"At some point, the pyramid will turn inside out and consume Dom [Howard]'s drum kit. Then Dom becomes a ninja who starts battling with corrupt businessmen… I'm serious. That's not a joke."
Former X Factor winner Matt Cardle last year cast doubt on the official version of events on September 11.
"The whole 9/11 thing... something's not quite right there," he claimed. "I think the way it was portrayed on TV and who was responsible and the way it happened was not the way it happened."
Watch the Muse 'Madness' music video below: