New Zealand's Green Party is calling for a Royal Commission of Inquiry into the country's spy agencies following revelations that investigative journalists are categorised as a threat to the nation and can therefore be spied on.

A leaked Defence Force manual obtained by the Sunday Star-Times lists "certain investigative journalists" as one of three main "subversion" threats, which qualifies them for surveillance.

The newspaper also reported that the New Zealand military allegedly received help from US spy agencies to monitor the phone calls of a New Zealand journalist in Afghanistan.

The Greens say the revelations are alarming and show a widespread culture of disregard for democratic values.

"The Defence Force is supposed to be there to protect New Zealand against foreign threats, instead it turns out that the Defence Force is turning its intelligence weapons against New Zealand journalists," Green Party co-leader Russel Norman said.

"If (Prime Minister) John Key and the intelligence and security services have been doing nothing wrong, then they have nothing to fear from a Royal Commission of Inquiry," Dr Norman said.

Thousands of people protested on Saturday against a bill widening spy agency powers.

The bill will make it legal for the foreign-focused Government Communications Security Bureau to spy on New Zealanders on behalf of the Security Intelligence Service, police and Defence Force.

The GCSB has carried out such surveillance in the past, believing it was legal, until last August when the Kim Dotcom court case raised questions about its legality - prompting Mr Key to change the law.

The Defence Force was contacted for comment but has not responded.