Dawn News reported sources said the meeting, which was held on the general's request, lasted for more than an hour.
Relations between civilian government and the military have been tense since revelations that Zardari had been behind a memo written by former Pakistan Ambassador to the United States Husain Haqqani reaching out to the U.S. government for help in averting a military coup in Pakistan and to help the civilian Pakistani government exert control over the country's armed forces.
The Press Trust of India reported Pakistani Prime Minister Syed Yousuf Raza Gilani appeared to extend an olive branch to the military. Gilani, with Kayani at his side, said all state institutions will be allowed to play their role, and called the armed forces a "pillar of nation's resilience and strength."
"It has been my government's policy to allow and enable all state institutions to play their role in their respective domains for the common good of the people," Gilani said at a meeting of the Cabinet.
"It is this desire to set good and healthy democratic traditions that has enabled us to seek strength from Parliament, which is the hallmark of a democratic government."
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