The cables released by WikiLeaks said that US special operations forces were embedded with Pakistani troops for intelligence gathering by the summer of 2009 and deployed with them on joint operations in Pakistani territory by September the same year.
The issue has gained heightened sensitivity in the wake of the US raid against Osama bin Laden in Abbottabad.
The revelations go against the Pakistani military's claim that it will not allow foreign troops to operate within the country for operations to flush out the Taliban and other militant elements.
"We have created intelligence fusion cells with embedded US special forces with both SSG and Frontier Corps (Bala Hisar, Peshawar) with the Rover equipment ready to deploy," then US Ambassador Anne Patterson was quoted by Dawn newspaper as saying in a cable to the US State Department in May 2009.
"Through these embeds, we are assisting the Pakistanis collect and coordinate existing intelligence assets," she said.
At the time, Patterson noted that the US had "not been given Pakistani military permission to accompany the Pakistani forces on deployments as yet."
By September, plans for joint intelligence activities had been expanded to include army headquarters.
"Pakistan has begun to accept intelligence, surveillance, and reconnaissance support from the US military for counter-insurgency operations," Patterson wrote.
"In addition, intelligence fusion centers" had been established "at the headquarters of Frontier Corps and the 11th Corps and we expect at additional sites, including the general headquarters and the 12th Corps in Balochistan", she said.
In April 2009, the cell at Bala Hisar assisted the Pakistan military operation then taking place in Lower Dir district of Khyber-Pakhtunkhwa province.
"US Special Operations Command Force are assisting the FC at the Intelligence Fusion Cell at FC Headquarters with imagery, target packages, and operational planning," a cable from that month said
A number of leaked cables reveal that the US was eager to embed American troops with Pakistanis soldiers. "On a brighter note, there is the possibility that operations in the northern Federally Administered Tribal Areas may provide additional opportunities to embed US Special Operations Forces with FC units to provide ISR (intelligence, surveillance and reconnaissance) support and general operational guidance," Patterson wrote in a November 2009 cable.
If we can expand on what we have recently been doing in Bajaur Agency with our embeds, it would be a significant opportunity to contribute to the pursuit of the TTP," she said.
The Bajaur operation with the Frontier Corps that Patterson referred to is likely one that was conducted in September 2009 and was described in an October 2009 cable previously published in the media. That cable also mentioned that US troops were deployed at Wana in South Waziristan and Miranshah in North Waziristan with the Pakistan Army's 11th Corps and that the Frontier Corps had requested a further deployment in Bajaur.
"Previously, the Pakistani military leadership adamantly opposed letting us embed our special operations personnel with their military forces. The recent approval by GHQ appears to represent a sea change in Pakistani thinking," the cable said.
"These deployments are highly politically sensitive. Should they receive any coverage in the Pakistani or US media, the Pakistani military will likely stop making requests for such assistance," it said.
Another previously published cable described how, in a January 2009 meeting with army chief Gen Ashfaq Parvez Kayani, then US Central Command chief Gen David Petraeus explained he "had given instructions that special operations forces would be deployed regularly and constantly, and the US 'needed to move their soldiers in here, so they could engage productively with the Frontier Corps'".
However, a deployment of US forces in Pakistani territory planned for April 2009 was called off at the last minute, according to another cable.
"The 3rd Commando Group of the Pakistan Special Services Group (SSG) exploited the weakened state of the Taliban surrounding Daggar, the main city within Buner (district of Khyber-Pakhtunkhwa), to secure the city early on April 29," the cable from the US Embassy in Islamabad said.
"Although reported that US officials would accompany the FC deployment to Daggar, a late-night decision on April 28 by the Pakistan Military General Headquarters denied the joint deployment, saying the FC had all the assets needed. Embassy will work with GHQ to determine the reason for the late change and to promote integrated operation support."
In the wake of the May 2 US raid that killed bin Laden in the garrison city of Abbottabad, the Pakistani military decided to reduce the US troop presence in the country to the minimum.