The controversy has erupted following the attempt on the life of Geo TV's leading anchor Hamid Mir on Saturday in Karachi.
Soon after the attack, Mir's brother came on the channel alleging that "certain elements" in the spy agency and its chief, Lt General Zaheerul Islam, orchestrated the attack, taking everyone by surprise.
The channel continued to play up the allegations but has off late distanced itself from it, saying the views were that of the family and what Mir had confided earlier.
Reports said the Ministry officials were hesitant to file the complaint but had to give in due to pressure from the army.
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The complaint, a copy of which was uploaded on the website of Committee to Protect Journalists, said "a vicious campaign, libelous and scandalous in nature was started initially on Geo News channel wherein false accusations were made" against a state institution and its chief.
It alleged that the entire campaign "was aimed at undermining the integrity and tarnishing the image of state institutions and its officers and falsely linking it with terrorists outfits/activities".
The footage was picked up by foreign media which instead of objectively reporting the incident "overplayed" it repeatedly, the complaint said.
Fakhruddin Mughal, spokesperson of PEMRA said the Defence Ministry has filed a complaint against the TV channel and its legal team was going through it.
"Yes, we have received the complaint. It is being examined by our legal team as in all cases. They will study it and give their recommendations which goes to our current 11-member Board. They may decide to agree with legal team's recommendation or not agree to," Mughal told PTI.