He was addressing a meeting of political leaders at the PM House, convened by Prime Minister Nawaz Sharif to allay fears that the court might be used against politicians.
Army spokesman Major General Asim Bajwa tweeted that General Raheel said army was not behind the military courts.
"Special courts not desire of the Army but need of extraordinary times. (We) will return to original system when normalcy returns," he tweeted.
He said Pakistan "can't even imagine to lose (it) as state or society".
He called upon the politician to take action as "our today's decisions will determine the destiny of our nation".
He said that the entire nation should be focused on their implementation of plan to root out militancy.
