The first "National Internal Security Policy", a copy of which was seen by AFP today, says that some of the country's 22,000 madrassas are responsible for spreading extremism.
Interior Minister Chaudhry Nisar Ali Khan presented the policy in parliament on Wednesday after a decade-long Islamist insurgency that has claimed thousands of lives and cost the economy "more than USD 78 billion".
On the topic of religious schools, the document says: "It is important to mention upfront that not all madrassas are a problem and therefore these must not be viewed negatively as a whole.
The vast majority of madrassas in Pakistan fall outside government control and offer little in the way of mainstream subjects for their students.
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"A large number of terrorists, either are, or have been students of madrassas where they were brainwashed to take up arms against the state," the paper said.
The 94-page policy document offers a candid and introspective look at where Pakistan has been failing in its efforts to fight terror.
It criticises the country's all-powerful military for being "unable to demonstrate other capabilities essential to successful counter-insurgency: hold, build and integrate", adding it is up to civil institutions to take up the slack.