The decision came following the AFP raid on the Canberra home of a News Corp journalist and the Sydney office of the ABC over separate leak investigations - both of which were widely condemned as heavy-handed and for having a chilling effect on reporting.

Mr Dutton said in a statement on Friday the direction to the AFP commissioner outlined the government's expectations in cases of leaks from former or current public servants.

It is understood the direction will apply to the News Corp and ABC investigations, as they are ongoing.

"A key function of the AFP is the enforcement of the criminal law, without exception," Mr Dutton said.

"However, I expect the AFP to take into account the importance of a free and open press in Australia's democratic society and to consider broader public interest implications before undertaking investigative action involving a professional journalist or news media organisation in relation to an unauthorised disclosure."

He said he expected AFP officers to "exhaust alternative investigative actions", and the voluntary cooperation of journalists and media organisations, before they considered further action.

As well, government departments and agencies will need to provide a "harm statement" - indicating the extent to which the disclosure is expected to significantly compromise Australia's national security - before referring a leak to the AFP.

Labor's home affairs spokeswoman Kristina Keneally said it had taken Mr Dutton too long to act.

She said it was still unclear whether any of the journalists under investigation would be charged for just doing their job.

"When it comes to freedom of the press and the public's right to know, Mr Dutton and the Morrison government have failed at every step of the way to show the leadership Australia deserves."

Australian Associated Press