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 here including the Pakistani Taliban, was yesterday 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 will 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.
Amir Mir, who is also a journalist, told Geo TV that his brother had told him two weeks back that if anything happens to him then "elements in the ISI and its chief Lt Gen Zaheerul Islam should be blamed".
Geo TV reported that Hamid Mir had confided the same to his friends, senior management of the channel, certain officials in the government and even the army.
The Pakistan military condemned the attack on Mir and sought an independent investigation.
A military spokesperson said that an independent inquiry must immediately be carried out to ascertain facts.
"However raising allegations against the ISI or head of the ISI without any basis is highly regrettable and misleading," the spokesperson said in a statement.
Doctors treating Mir have said he is out of danger.