The report is based on interviews with Taliban commanders in Afghanistan, and was written by Matt Waldman, a fellow at Harvard University.
US officials have long suspected a link between the ISI and the Taliban, but those suspicions are rarely confirmed.
"Pakistan appears to be playing a double-game of astonishing magnitude," the report said.
A Pakistani diplomatic source dismissed the report as "naive".
Asad Durrani, a former head of the ISI, told Al Jazeera that he does not believe the report, and that intelligence agencies are supposed to maintain relationships with groups like the Taliban.
Durrani also dismissed the claim that ISI representatives met with the Quetta Shura, calling it "nonsense".
The report also links high-level members of the Pakistani government with the Taliban.
It claims Asif Ali Zardari, the Pakistani president, met with senior Taliban prisoners earlier this year and promised to release them. Zardari reportedly told the detainees they were only arrested because of American pressure.
Matt Waldman, the study's author, discusses his methodology in an interview with Al Jazeera
"The Pakistan government's apparent duplicity - and awareness of it among the American public and political establishment - could have enormous geopolitical implications," Waldman said.
"Without a change in Pakistani behaviour it will be difficult if not impossible for international forces and the Afghan government to make progress against the insurgency."
Afghan officials have long been suspicious of the ISI's role.
Amrullah Saleh, the former director of Afghanistan's intelligence service, told Reuters last week that the ISI was "part of a landscape of destruction in this country". Saleh resigned last week over a dispute with Hamid Karzai, the Afghan president.
Even Karzai himself has in the past accused the ISI of working with the Taliban.
"These allegations have been made so many times in the past," said Al Jazeera's James Bays, reporting from Kandahar.
"The debate is whether it's a formal involvement with Pakistani authorities, or whether these are just people left over in the Pakistani government who have their old connections [to the Taliban]."
The report comes as Nato and Afghan officials are preparing for a major offensive against the Taliban in Kandahar province in southern Afghanistan.