Musharraf said there was no blanket agreement with the US on the controversial drone campaign and that his regime had cleared missile strikes "only on very few occasions where the target was absolutely isolated and (the drone strike) had no chance of collateral damage".
The drone strikes were discussed "at the military (and) intelligence level" and cleared only if "there was no time for our own (special operations task force) and military to act", he said. "That was...maybe two or three times only," he told CNN in an interview.
Sometimes, he said, "you couldn't delay action". He added: "These ups and downs kept going...It was a very fluid situation, a vicious enemy...mountains, inaccessible areas".
Musharraf said that one of those killed by US drones was Nek Mohammed, a tribal warlord accused of harbouring al-Qaeda militants in the tribal belt.
At the time, in June 2004, Pakistan intelligence said Mohammed died after Pakistani forces launched a missile at a house where he was staying.
Pakistani leaders have for long denied the country's involvement in clearing drone strikes. The Foreign Office described the strikes as counter-productive for the war against terrorism and a violation of Pakistan's sovereignty.