According to Federal Information Minister Marriyum Aurangzeb, the commission will be headed by a high court judge.
The announcement came as the Islamabad High Court refused to make a judicial commission saying that there is no point to constitute the commission at this stage.
The judicial panel can include members from civil society and the media.
The prime minister assured the nation that there will be a fair and transparent investigation and the facts will be brought before the people.
The GHQ, meanwhile, sent a letter to the federal government and asked to form an inquiry commission to investigate the murder of Arshad Sharif in Kenya.
The letter also requested legal action against the accusers as per the constitution of Pakistan.