He also promised to probe allegations about ISI's involvement in his abduction.
Malik's assurance came while speaking to the media after visiting Shahzad's residence in Islamabad. At the same time, Malik said the journalist's murder could be a "case of personal enmity".
Ali Dayan Hasan, the Human Rights Watch representative in Pakistan, has told the media that he suspected that Shahzad had been picked up by the ISI.
Shahzad, 40, who worked for an Italian news agency and an online news website registered in Hong Kong, went missing on Sunday. His body was found at Mandi Bahauddin in Punjab province.
Shahzad disappeared two days after writing in an investigative report in Asia Times Online that al-Qaeda carried out a recent attack on a naval airbase in Karachi to avenge the arrest of naval officials suspected of having links to the terrorist group.
Malik said Shahzad's family was not satisfied with the autopsy report and had demanded that a second post-mortem examination should be conducted.
"Though another autopsy is not possible, a medical board can be formed to carry out investigations," he said.
Pakistani journalists, like the army, are battling negative forces, Malik said. To ensure their safety, orders have been issued to allow journalists to carry small arms for self-defence, he said.