Chaudhry Nisar Ali Khan told reporters outside the Parliament House that it was the government's constitutional and legal responsibility to protect the dignity of the Pakistan Army and other intelligence agencies, adding that there should be no ambiguity or fallacy in that respect.
The controversy erupted after Mir's brother accused "certain elements" in the ISI and its chief of orchestrating the attack, a charge denied by the military.
Current affairs talk show host Mir, 47, is recovering after being shot at least three times in his car in Karachi last Saturday.
The Defence Ministry has filed a complaint before the electronic media regulatory authority seeking cancellation of Geo TV's license.
More From This Section
Media reports said Geo TV has been blocked in military establishments here and many cable network operators have pushed it down the queue.
Khan said he was personally trying to ensure that the situation would not be aggravated by either sides.
He said the ISPR (Inter Services Public Relations) had strongly condemned the attack on Mir and also demanded for an independent commission to probe the incident, adding that a media trial would create further confusion.
He said an independent media as well as honourable and dignified armed forces were the needs of Pakistan. He advised both sides to remain patient and to avoid troublemakers.
Khan said Mir's family should come forward in case of any doubts over the Sindh police's investigation and the commission set up to probe the attack and that alternate options could be considered.