A report detailing the killing of al-Qaeda's second-in-command Abu Muhammad al-Masri also shed light on the regime's efforts to protect the terrorist leader in an upscale suburb of Tehran for years.
Religious scholars welcomed the move, saying that the registration process will help in delinking ties between some madrassas and proscribed terror outfits.
While both groups specialise in deadly violence and terror as a means to territorial expansion, their ideologies differ so fundamentally that they are increasingly killing each other.
The attack on the madrassa brings back memories of the 2014 terrorist massacre at the Army Public School in Peshawar.
The insurgent outfit may attempt to target political and religious leaders in Quetta and Peshawar, according to the warning.
Gunmen killed at least six people in Balochistan, while a improvised explosive device blast killed six security personnel in Waziristan.
Tehran's efforts to stoke upheaval in Pakistan are part of its overall plan to destablise and dominate the region, said a top leader of the Iran-based militant group Jaish al-Adl.
As Islamabad seeks potential assistance from Washington, recent tensions between the United States and China may offer an opportunity for Pakistan to improve its economy.
The Federal Board of Revenue is continuing to break up networks and arrest suspected financial backers of militant outfits.
'With the alliance, the insurgency here is likely to escalate here in coming days,' said one defence analyst.