According to the BBC, the London School of Economics (LSE) report claims that the ISI is providing funding, training and sanctuary to the Taliban on a scale much larger than previously thought.
The report's unnamed author concludes that Pakistan's relationship with the insturgents runs far deeper than previously realised.
Some of the commanders interviewed suggested that the ISI even attends meetings of the Taliban's supreme council.
They claim that by backing the insurgents Pakistan's security service is trying to undermine Indian influence in Afghanistan.
The report concludes that without a significant change in approach by Pakistan, both the Afghan government and international community will find it impossible to end the insurgency in Afghanistan.
The spokesman for Pakistan's military said the claims were "rubbish" and part of a malicious campaign against the country's military and security agencies.