A formal request will be made to the Supreme Court Chief Justice to nominate three members of the commission, a statement released by the Prime Minister's Office said.
Mir, 47, who faced threats from multiple quarters, including the Pakistani Taliban, was on Saturday shot at in Karachi by four unidentified gunmen.
He sustained three bullet injuries in his leg and pelvic area after he was fired upon near Natha Khan bridge soon after he left Karachi airport for his office. He was rushed to hospital where he was operated upon for over three hours.
The government has offered a reward of Rs. 10 million for any information that leads to the arrest of the attackers.
Information minister Pervaiz Rashid, who visited Mir in the hospital, said the government is working to strengthen the democratic culture in the country.
He said the responsibility of investigations into the attack on Mir lies on the Sindh government.
However, he said that the federal government would extend full cooperation to the provincial government for the same.
Mir's brother has accused "elements in the ISI" of orchestrating the attack on him, a charge denied by the military.