His leaving is apparently driven by a desire to capitalise on the growing market for cyber security specialists in the private sector.
The Australian reported that MacGibbon's leaving would be announced by the government on Saturday.
MacGibbon, 51, was formerly a member of the Australian Federal Police and spent 15 years in the force.
Under the reorganisation of government departments which led to the creation of the Home Affairs Department, his role has assumed more importance.
The Australian quoted Home Affairs Minister Peter Dutton as saying of MacGibbon, that he was “one of the best in the business”.
“He has made a decision to move from the public service to the private sector,” Dutton said.
“I have worked very closely with Alastair over a long period of time and have the utmost respect for his professionalism and expertise. I wish him every success in the next stage of his professional life.”