Home Affairs Minister Peter Dutton has flagged a boost to Australia's counter-espionage efforts and a greater domestic focus for the Defence Department's cyberspy agency as he moves to put his stamp on the new super-portfolio.

Speaking after he was sworn in as the minister in charge of a wide range of agencies, Mr Dutton said that terrorism would remain the top focus but battling espionage had been "well and truly underdone" in the era of al-Qaeda and the so-called Islamic State.

And he said the Australian Signals Directorate - which primarily exists to support Defence by gathering foreign electronic intelligence - would be used more in Australian investigations into terrorism, drug-smuggling, child exploitation and other cross-border crimes.

"I think people will quickly understand what Home Affairs is about and the virtue of it when you see the element of the Australian Signals Directorate that has a cyber capacity that is now working more closely with the anti-gang members of the Australian Federal Police that are targeting an offshore venture," he said.