Mr 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. That was...maybe two or three times only," he told CNN.
Sometimes, he said, "You couldn't delay action," adding: "These ups and downs kept going...It was a very fluid situation, a vicious enemy...mountains, inaccessible areas."
Mr Musharraf returned to Pakistan from self exile last month to contest the general elections in May.
He said that one of those killed by US drones was Nek Mohammed, a tribal warlord accused of harbouring Al Qaeda militants in the country's tribal belt.
At the time, in June 2004, Pakistan intelligence had said Nek 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.
Hundreds of people have been killed in drone strikes since 2004, including top Taliban and Al Qaeda operatives.
Mr Musharraf's admission suggests he and others did play some role even if they did not oversee the programme or approve every attack, the CNN reported.
His admission that Pakistani leaders agreed to even a limited number of strikes runs counter to Islamabad's frequent denunciation of the drone campaign.
In a 2008 diplomatic cable made public by WikiLeaks, then US Ambassador Anne Patterson mentioned a discussion about drones during a meeting with then Interior Minister Rehman Malik and then premier Yousuf Raza Gilani.
"Rehman Malik suggested we hold the alleged Predator attacks until after the Bajaur operation," she wrote. "The PM brushed aside Rehman's remarks and said, 'I don't care if they do it as long as they get the right people. We'll protest in the National Assembly and then ignore it'."