The messages were sent through SMS to the members of both houses of parliament and the four provincial assemblies recently, he said, adding investigations were on to trace the culprits.
"With the help of the Cyber Crime Wing, two people have been arrested in this regard from Larkana (in Sindh). According to a preliminary investigation, the culprits misused the identity cards of these detained persons," he said.
"It is strange how the culprits managed to get the contact numbers of the VIPs," Malik said.
Malik told reporters on the sidelines of an event here that the matter was being probed and the Cyber Crime Wing will soon indentify the persons involved in sending the messages so that legal action can be taken against them.
He further said the issue of a secret memorandum sent purportedly by the civilian leadership to the US administration will be "open for investigation" if required.
Pakistan's Ambassador to the US Husain Haqqani has been called to Islamabad to explain the issue, he added.
Replying to questions regarding Red Corner Notices issued by Interpol for persons linked to the killing of former premier Benazir Bhutto and Baloch nationalist leader Akbar Bugti, Malik said concerned officials had been directed to interact with the international police agency.
Pakistan's investigation into Bhutto's assassination is continuing, he said.