Addressing a press conference in Kabul on his first visit to Afghanistan, Musharraf ruled out joint operations with US troops to flush out terrorists hiding in Pakistan.
Musharraf was referring to recent raids in Lahore and Faislabad in the Punjab province, which led to the arrest of nearly sixty terrorists.
Abu Zubaida, a top Al Qaeda official, is suspected to be among those detained.
The Pakistani president presented a check of $10 million in aid to Afghanistan's interim leader Hamid Karzai.
More reports on US war on terror
More reports on Pakistan
Tell us what you think of this report