"Pakistan's involvement with jihadi terror groups initially was primarily done as a strategic investment, which was supposed to bring them benefits through influence in Afghanistan and to be used against India in Jammu and Kashmir. That has backfired," said Mr Haqqani.
"Now even though it has backfired, Pakistan has been very selective in going after these jihadi terror groups. That is the reason why the jihadis pick specific targets like Shias, Ahmadis or Christians, to improve their recruitment, playing on various kinds of polarisation, and taking advantage of that," he said.
"The real problem lies in that attitude of the Pakistani government of trying to protect the parties in Pakistan's Punjab province, while going after the terrorists in other parts of the country, but not in Pakistani Punjab province. That's what has come back to bite them," he said.
Mr Haqqani said "the fact of the matter is that the Pakistani military and civilian leadership easily gets distracted by delusions of fighting India and its influence in Afghanistan and allowing certain jihadi terror groups to pursue those objectives, not realising that they can end up having offshoots, just like the Pakistani Taliban emerged out of the Afghan Taliban."
"The Pakistani component of the Afghan Taliban ended up becoming a separate group. And now Jamaat-ul-Ahrar has broken away from the Pakistani Taliban. Pakistan has to make a decision to go after all terrorist groups, as well as the mindset that breeds these terrorists. And Pakistan has not been able to make that decision," he said.
Jamaat-ul-Ahrar claimed responsibility for Sunday's grisly suicide attack in Lahore that killed 72 people.
"The state has not taken any of the measures that are necessary to isolate them (terror group). So, there are groups like Lashkar-e-Taiba and Jaish-e-Mohammed which attack India. They are spared. Once they are spared, it's very possible that some of their members will actually join splinter groups which will also attack Pakistan," he said.