Hunting bin Laden
Scahill, citing military intelligence sources and a former Blackwater official, said the programme began with an agreement between the US and Pakistani governments.
"In 2006, the Bush administration struck a deal with the government in Islamabad that would allow US special forces to actually enter Pakistani territory if what they were doing was hunting Osama bin Laden or his top deputies.
"The agreement was such that the Pakistanis said that they would have the right to deny that they had given permission."
There was no immediate comment from Islamabad on the story, and Scahill said that the White House also failed to respond to his request for comment.
But he said the office of Admiral Mike Mullen, the chairman of the US Joint Chiefs of Staff, had contacted him to reject the allegations.
"I did not call them, they called me and told me that the [allegations] did not stand up to reality," Scahill said.
"I've talked to my sources though, and they say that it's possible that officials within the military chain of command are simply not in what [they] called 'the circle of love' on this programme."
US officials have said that they believe northwest Pakistan is a hiding place for al-Qaeda fighters, including Osama Bin Laden.
The northwest tribal region, and in particular Peshawar, the capital of the North West Frontier Province (NWFP), have borne the brunt of attacks perpetrated by the Taliban in recent weeks.
The attacks are in apparent retaliation for a military offensive launched in the country's semi-autonomous tribal region of South Waziristan against members of the Tehreek-e-Taliban Pakistan, one of the main anti-government groups.
But a spokesman for the Taliban last week blamed Blackwater for at least two of the recent bombings.
Azam Tariq posted a video statement on the internet, saying the Taliban attacks never aimed to target civilians and that the explosions were linked to Blackwater activities in the country.
Xe has denied having any contracts in Pakistan.
The North Carolina-based firm provides security for diplomats around the world, but it is facing charges of human rights violations stemming its part from a 2007 shooting in Iraq that left 17 civilians dead.