ISLAMABAD, Pakistan (CNN) -- Ex-Pakistani President Pervez Musharraf acknowledged his government secretly signed off on U.S. drone strikes -- the first time a top past or present Pakistani official, who have longed condemned the U.S. program, has admitted publicly to such a deal.

In an interview this week in Islamabad, Musharraf insisted Pakistan's government signed off on strikes "only on a few occasions, when a target was absolutely isolated and no chance of collateral damage."

Still, his admission that Pakistani leaders agreed to even a limited number of strikes runs counter to their repeated denunciations of a program they long claimed the United States was operating without their approval. The drone strikes -- which the nonpartisan public policy group New American Foundation estimates have killed at least 1,990 people in Pakistan, including hundreds of civilians -- are unpopular in Pakistan.

"Today, the world superpower is having its own way, without any consent from Pakistan," former Interior Minister Rehman Malik said last month.

Pakistani leaders have long openly challenged the drone program and insisted they had no role in it. Yet there's been speculation that the story might have been different behind the scenes.

In a cable sent in August 2008 and later posted online by Wikileaks, then-U.S. Ambassador to Pakistan Anne Patterson mentioned a discussion about drones during a meeting that also involved Malik and then-Prime Minister Yousuf Raza Gilani.

"Malik suggested we hold off alleged Predator attacks until after the Bajaur operation," Patterson 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.' "

Unmanned U.S. drones began launching attacks in Pakistan in 2004, by which time Musharraf had been president for five years after taking power in a bloodless coup.

He said that Pakistani leaders would OK U.S. drone strikes after discussions involving military and intelligence units and only if "there was no time for our own ... military to act."

This happened "only rarely," said Musharraf, who left office in 2008 and spent years in exile before returning to Pakistan last month to launch a political comeback. But sometimes, he said, "you couldn't delay action."

"These ups and downs kept going," he said. "It was a very fluid situation, a vicious enemy, ... mountains, inaccessible areas."

Musharraf said that one of those killed by U.S. drones was Nek Mohammed, a tribal leader accused of harboring al Qaeda militants in Pakistan's western border region. At the time, in June 2004, Pakistan intelligence sources said Mohammed died after Pakistani forces launched a missile at a house where he was staying.

CNN's Nic Robertson reported this story from Pakistan, and Greg Botelho wrote it in Atlanta.