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A former intelligence officer who served in Afghanistan said Pakistan has allowed the U.S. to create CIA/Joint Special Operations Command safe houses inside the country to hunt down militants. The CIA/JSOC fusion has led to the capture and deaths of scores of al Qaeda militants, including bin Laden.

“We based drones at several of their air bases that have resulted in a lot of [al Qaeda deaths],” the former officer said. “They have allowed transit of equipment via rail and via air through Pakistan en route to Afghanistan.”

This source said Pakistan views al Qaeda has a gang of Arab outsiders who threaten the regime, whereas the Haqqani Network has tribal ties to officials inside the armed forces and government.

“Basing rights and the establishment of logistics routes into Afghanistan have been the two most important aspects of our partnership since 9/11,” said an Army Special Forces officer. “It could be argued that those things are the only reasons we pretend there is a partnership at all.”

Intelligence sharing, however, remains spotty, since the CIA believes information passed to Islamabad on certain targets ends up as a tip-off to militants to change locations.

“They have assisted in the apprehension of terrorists, but I believe they were very selective on if or when to help in such operations,” the Army officer said.

The Obama administration has embarked on a $7.5 billion economic aid program over five years to build schools, improve electricity and spur economic growth in Pakistan.

But the Government Accountability Office reported this year that only a small portion had been spent over fears that Pakistani government corruption was diverting the money.

In July, the New York Times reported the administration was withholding hundreds of millions of dollars in military aid in protest over Pakistan’s failure to launch promised counterterror operations and its refusal to allow new U.S trainers into the country.

The Congressional Research Service reports that Congress has appropriated more than $22 billion in economic and security-related aid to Pakistan since 2002.

James Phillips, a Middle East analyst at the Heritage Foundation, said Pakistan aids militants such as the Haqqani Network because it fears a Pashtun-dominated Afghanistan will one day form an alliance with India.

“To preclude such an alliance, the Pakistani military historically has encouraged Islamist radicals inside Afghanistan because it knows that they will be willing allies against India and will be less likely to foment a Pashtun nationalist rebellion inside Pakistan,” Mr. Phillips said.

He said Pakistan’s Inter-Services Intelligence (ISI), which helped bring the Taliban to power, is eyeing President Obama’s 2014 troop exit date from Afghanistan as a time to re-exert power across the border.

“The ISI, which controls Islamabad’s Afghanistan policy, works covertly with the Taliban, Haqqani Network and other insurgent groups to gain a hammerlock on Afghan politics after the U.S. withdraws,” Mr. Phillips said. “Regrettably, by emphasizing the exit timetable arbitrarily imposed on the U.S. troop surge, the Obama administration has encouraged ISI’s belief that Washington is only concerned with rushing for the exit and that it can continue its duplicitous policy with little consequence for the bilateral relationship.”