The report, 'Separating the Taliban from al-Qaeda: The core of success in Afghanistan,' argued that Pakistan was hesitant to take on the Taliban and al-Qaeda as they regarded the government in Kabul as too close to India.
"They regarded the government in Kabul as too close to India and maintained the former rulers they had supported as a tool of pressure to protect Pakistan’s security interests," said the report published by New York University.
"From a Pakistani perspective, the post-2001 period was a balancing act in which publicly expressed interests differed from those expressed privately," according to the report by Alex Strick van Linschoten and Felix Kuehn.
It said General Pervez Musharraf and other officials "made numerous public statements pledging support for US goals, but at the same time drew private conclusions that the interests of Pakistan were not best served by moving against the Taliban and their associates".
The main focus of the article, however, is to underline the differences between al-Qaeda and Taliban, and to recommend engagement with the latter as a way to end the conflict in Afghanistan.
"Elements of the Pakistani state also thought they could use an insurgency in Afghanistan as pressure against the Afghan government and the US," the report said.
"Al-Qaeda has had little or no influence on the origin and course of the insurgency, though it has assisted with training and fund raising," it said.
Both authors have lived and worked in Afghanistan for several years.
The New York Times described them as being "among a small group of experts who say the only way to end the war in Afghanistan is to begin peace overtures to the Taliban."
"There is room to engage the Taliban on the issues of renouncing al-Qaeda and providing guarantees against the use of Afghanistan by international terrorists in a way that will achieve core US goals," the report said.
It said that Taliban leaders were not in the loop about the 9/11 attacks but the authors noted that Taliban chief Mullah Omar's decision to protect al-Qaeda chief Osama Bin Laden was "difficult to rationalise."
But it was in part because Mullah Omar thought he had Pakistan's support before the US attacked following the 9/11 terror strikes.
"He believed that the Taliban's standing in the Islamic world depended on resisting US demands about bin Laden," the report said.