The study by the RAND corporation, funded by the US Department of Defense, finds that if Taliban bases in Pakistan are not eliminated, the forces supporting the government of Afghan President Hamid Karzai "will face crippling long-term consequences in their effort to stabilize and rebuild Afghanistan."
The study, titled "Counterinsurgency in Afghanistan," says that Pakistan's Inter-Services Intelligence Directorate and paramilitary Frontier Corps "have failed to root out Afghan insurgent groups based in Pakistan and, in some cases, individuals from these Pakistani organizations have provided direct assistance to such groups as the Taliban and Haqqani network."
According to the report's author, Seth Jones, the Taliban and other groups "are getting help from individuals in Pakistan's government, and until that ends, the region's long-term security is in jeopardy."
Other groups such as Al Qaeda and Gulbuddin Hekmatyar's radical Islamic Hezb-i-Islami organisation are also getting support in Pakistan, according to the study.
It says the insurgents find refuge in Pakistan's Federally Administered Tribal Areas, North West Frontier Province and Baluchistan province.
"They regularly ship weapons, ammunition and supplies into Afghanistan from Pakistan, and a number of suicide bombers have come from Afghan refugee camps based in Pakistan," the report says.
The Taliban were removed from government in a US-led invasion of Afghanistan in late 2001 and are waging an insurgency that has gained pace the last two years.
There are nearly 70,000 foreign soldiers from more than 40 nations attached to NATO's International Security Assistance Force, helping the growing Afghan army and police force tackle the insurgents and rising crime.
Islamabad has signed a peace deal with pro-Taliban militants in the Swat Valley, about 99 kilometres (61 miles) from Afghanistan, which has seen soldiers leave the area and the rebels implementing Islamic Sharia law.
The Pakistani government is in talks with Al Qaeda-linked leader Baitullah Mehsud, who has vowed to continue "jihad" (holy war) in Afghanistan while pursuing peace negotiations.
In Kabul on Friday, Pakistan's foreign minister Shah Mahmood Qureshi said that his government was not in talks with "terrorists" but only with "peace-loving" elements as part of a multipronged strategy to fight extremism.