"The political parties have agreed to establish military courts after almost 11 hours of deliberations," a senior government official told AFP, requesting anonymity.
He said all terrorism related charges will be dealt with by the military courts.
The resolution was confirmed by another senior government official and a political leader who attended the meeting.
The parties met to chart out a plan to combat terrorism after the attack last week on a military-run school in the northwestern city of Peshawar that killed 150 people, mostly schoolchildren.
Pakistani civil society activists light candles during a rally in Karachi on December 23, 2014, held in solidarity with the victims of the Peshawar school massacre. (Getty)
Leader of the opposition Syed Khursheed Shah said the military courts will be established for a term of two years.
"Only terrorists would be tried in these courts and these would not be used for political objectives," he told AFP.
"The aim of setting up military courts is to ensure the speedy trial of terrorists, there are so many loopholes in our judicial system and it has failed to deliver," Shah said.
He said the all the political parties had agreed to amend the constitution to facilitate the establishment of the military courts.
The meeting also passed a unanimous resolution condemning the attack last Tuesday which was the deadliest in the history of the country.
Following the assault, Prime Minister Nawaz Sharif ended a six-year moratorium on the death penalty, reinstating it for terrorism-related cases.
Pakistan has described the bloody school rampage, claimed by the Tehreek-e-Taliban Pakistan (TTP), as its own "mini 9/11", calling it a game-changer in the fight against extremism.
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