Pakistani intelligence gives funding, training and sanctuary to the Afghan Taliban on a scale much larger than previously thought, a report says.
Taliban field commanders interviewed for the report suggested that ISI intelligence agents even attend Taliban supreme council meetings.
Support for the Afghan Taliban was "official ISI policy", the London School of Economics (LSE) authors suggest.
Pakistan's military denied the claims.
A spokesman said the allegations were "rubbish" and part of a malicious campaign against the country's military and security agencies.
The LSE report comes at the end of one of the deadliest weeks for Nato troops in Afghanistan, with more than 30 soldiers killed.
Links between the Taliban and Pakistan's intelligence service have long been suspected, but the report's author - Harvard analyst Matt Waldman - says there is real evidence of extensive co-operation between the two.
"This goes far beyond just limited, or occasional support," he said. "This is very significant levels of support being provided by the ISI.
"We're also saying this is official policy of that agency, and we're saying that it is very extensive. It is both at an operational level, and at a strategic level, right at the senior leadership of the Taliban movement."
Mr Waldman spoke to nine Taliban field commanders in Afghanistan earlier this year.
Some alleged that ISI agents had even attended meetings of the Taliban's top leadership council, the so-called Quetta shura. They claim that by backing the insurgents Pakistan's security service is trying to undermine Indian influence in Afghanistan.
"These accounts were corroborated by former Taliban ministers, a Western analyst and a senior UN official based in Kabul, who said the Taliban largely depend on funding from the ISI and groups in Gulf countries," the report said.
With US troops due to begin leaving next year, Pakistan and other regional players are increasingly seeking ways to assert their influence in Afghanistan, analysts say.
Pakistan has long been accused of using the Taliban to further its foreign policy interests in the country. The ISI first became involved in funding and training militants in Afghanistan after the Soviet invasion in 1979.
Since 2001, however, it has been a key US ally, receiving billions of dollars in aid in return for helping fight al-Qaeda
"Pakistan appears to be playing a double-game of astonishing magnitude," the report says.
But Islamabad says it is working with its international partners in hunting down the Taliban.
And the Taliban's former ambassador to Pakistan, Abdul Salam Zaeef, says there is no proof of a link between the ISI and the Afghan Taliban.
"I have no proof that Pakistan is supporting the Taliban," he told the BBC, "or that the ISI is providing money to them... or other support to provide weapons."
Even so, Pakistan's role in Afghanistan is viewed as critical.
Last week Afghan intelligence chief Amrullah Saleh resigned, saying he had become an obstacle to plans to talk to the Taliban.
Mr Saleh told Reuters news agency a day after quitting that the ISI was "part of the landscape of destruction" in Afghanistan and accused Pakistan of sheltering Taliban leaders in safe houses.
Pakistan has always denied such claims and points to arrests and military offensives against the militants on its side of the border. Nevertheless, parts of the tribal north-west of Pakistan bordering Afghanistan remain strongholds for the militants.
The BBC's Quentin Sommerville in Kabul says there is a growing understanding that military action alone will not be enough to bring peace in Afghanistan.
"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," the report concludes.