The leaked report, derived from thousands of interrogations, claims the Taliban remain defiant and have wide support among the Afghan people.
A BBC correspondent says the report is painful reading for international forces and the Afghan government.
A Pakistani foreign ministry spokesman called the accusations “ridiculous”.
“We are committed to non-interference in Afghanistan and expect all other states to strictly adhere to this principle,” Abdul Basit told the BBC.
“A stable and peaceful Afghanistan is in our own interests. We cannot indulge in any activity which takes us away from achieving that objective,” he added.
The report alleges that Pakistan knows the locations of senior Taliban leaders.
“We have long been concerned about ties between elements of the ISI [Pakistan’s intelligence service] and some extremist networks,” said US Pentagon spokesman Captain John Kirby, adding that the US Defence Department had not yet seen the report.
Pakistan Foreign Minister Hina Rabbani Khar is currently in Kabul for talks with Afghan President Hamid Karzai.
The BBC’s Quentin Sommerville in Kabul says the report – on the state of the Taliban – fully exposes for the first time the relationship between the ISI and the Taliban.
The report is based on material from 27,000 interrogations with more than 4,000 captured Taliban, al-Qaeda and other foreign fighters and civilians.
It notes: “Pakistan’s manipulation of the Taliban senior leadership continues unabatedly”.
It says that Pakistan is aware of the locations of senior Taliban leaders.