The president said he hoped the results of the investigation would be published before February's parliamentary vote.
Musharraf said the parliamentary elections, which were were delayed following Bhutto's killing on Dec 27 and rescheduled for Feb 18, would be held, no matter "what happens."
Bhutto's son, Bilawal, has said he does not believe that a government inquiry into his mother's death has had the "necessary transparency."
Musharraf said there was a campaign by al-Qaeda to undermine Pakistan, but denied the country was about to disintegrate and descend into violence.