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U.S. officials say ISI continues to maintain linkages to militant groups, including the Pakistani Taliban, LeT and the Haqqani Network.

These concerns were reinforced by the confession of Pakistani American David Coleman Headley on the role the ISI played in planning the Mumbai operation. Headley pleaded guilty to helping LeT carry out the Mumbai attacks by carrying out surveillance of targets.

A U.S. official, speaking on the condition of anonymity due to the sensitive nature of the information, said terrorist safe havens in Pakistan are not confined to the northwestern region straddling the border with Afghanistan.

“There are terrorists in Pakistan outside the frontier areas, which is definitely contributing to the threat against U.S. troops in Afghanistan and against Pakistan itself,” the U.S. official said.

A second U.S. official, who also spoke on the condition of anonymity, said: “Everyone’s eyes are wide open … to the complexities of the Pakistanis’ historical relationships with certain players in the region.”

In his new memoir “Decision Points,” former President George W. Bush writes that some in the ISI retained close ties to Taliban officials, while others wanted an insurance policy in case the U.S. abandoned Afghanistan and India tried to gain influence there.

In 2005 and 2006, sanctuaries in Peshawar and Quetta aided the rise of the insurgency, Mr. Bush said.

By 2008, he got tired of reading intelligence reports about terrorist sanctuaries in Pakistan and hinted that he sanctioned the covert Predator drone strikes in Pakistan.

“Over time, it became clear that Musharraf either would not or could not fulfill all his promises” to deny al Qaeda safe haven in Pakistan and break ties with the Taliban, Mr. Bush writes, adding that part of the problem was Pakistan’s “obsession with India.”

Mr. Musharraf described Kashmir as the root cause of terrorism in the region and lamented the fact that Mr. Obama did not raise the issue on his recent visit to India. “The solution is the resolution of the Kashmir dispute. Not because Pakistan wants it, it is necessary for the world to fight terrorism and extremism,” the former Pakistani leader said.

On the use of Predator drones to kill militants hiding in Pakistan’s tribal areas, Mr. Musharraf said the use of the unmanned aerial vehicles pose a dilemma since the drones kill militants but their indiscriminate use has caused collateral damage.

Mr. Musharraf, who has launched his own political party, is exploring the possibility of returning to Pakistan and running for the office of president — a position he held for seven years after seizing power in a bloodless coup in 1999. He was forced to resign in 2008.