He said that the operations, which mainly occurred between 2003 and 2008, involved helicopter-borne elite troops secretly crossing over the borders, without informing the Pakistani authorities.
"The Pakistanis were kept entirely in the dark about it. It was one of those things we wouldn't confirm officially with them," said the source, who had detailed knowledge of the operations.
The Pakistani public opinion has grudgingly tolerated the American drone strikes, and even the minutest hint of any physical presence of US soldiers within their borders would have surely welcomed strong denunciation.
However, the clandestine nature of the raids underscores the suspicious nature of the relationship between the two allies.
Destroying the Taliban safe haven inside Pakistan is the unspoken part of US President Barack Obama's 'surge' announced this month. Although 30,000 troops will be deployed to Afghanistan by next summer, the Taliban and the Al Qaida leadership is believed to be sheltering on the Pakistani side of the border.
In recent weeks, US has sent a number of senior officials to Islamabad seeking Pakistani action on at least two fronts: attacks on Sirajuddin Haqqani, a warlord with strong Al Qaida ties based in North Waziristan, and an expansion of the Central Intelligence Agency-led drone strikes into the western province of Balochistan.
"This is crunch time," said a senior Pakistani official. "The tone of the Obama administration is growing more ominous. The message is 'you do it, or we will'."
The US demands have apparently drawn an angry reaction from Pakistan's military. A senior official with Pakistan's spy agency Inter-Service Intelligence said it was hunting the Taliban in Balochistan, citing 60 joint operations between the CIA and ISI in the province over the past year.
"They are going in for kills, they are apprehending people," he said. The official, who spoke anonymously but with official sanction, said Pakistan's military were overstretched. "We can't fight everywhere at once," he added.
The ISI official further accused the US of 'scapegoating' Pakistan for its own failures.
The CIA declined to comment on this.