Calls of Stephenson's associates were also monitored.
The monitoring was believed to have been co-ordinated from the main US intelligence centre at Bagram, north of Kabul. According to the article, GCSB staff have been posted at this unit since early in the Afghanistan war.
Information exposing the spying had been obtained from anonymous "sources".
Comment is being sought from the Defence Force.
The reports of monitoring follows a case in which Stephenson sued the Defence Force for defamation in the High Court at Wellington after the Defence Force denied details in several of his articles regarding activities of the organisation's personnel in the Afghanistan war.
The jury could not reach a verdict and Stephenson has yet to decide whether to seek a retrial.
The Defence Force has accepted Stephenson had been at an Afghanistan base and conducted interviews but has yet to issue a statement correcting it.
An internal Defence Force manual, which refers to "certain investigative journalists", as "subversion" threats was also referenced by Hager's article.
The manual, which was leaked, was issued as an order by the head of the Defence Force.
The manual said some journalists may be classed as hostile individuals as they pose a threat of subversion, according to the article.
"Counter intelligence" methods, which are "activities concerned with identifying and counteracting the threat to security" by such individuals or organisation can be sanctioned by the by the Defence Force chief in New Zealand.
The Green Party called for inquiry to look into New Zealand intelligence services following the reports of spying on Stephenson.
"These new revelations that the NZDF categorise journalists as subversives is alarming. It is time for a Royal Commission into New Zealand's intelligence services in order to protect our democracy, our freedom, and our free press," co-leader Dr Russel Norman said.
Prime Minister John Key said he did not know anything about Stephenson being monitored by the Defence Force aided by US agencies while in Afghanistan.
"I haven't had any advice that he is and I'd want to see facts in support of that to see if it's true."
He said if that was the case he would be asking why it had happened.
Mr Key said he had already had questions about Stephenson in relation to the Government Communications Security Bureau (GCSB) put to him last week.
"The advice I've had from the GCSB is that he isn't a target and has never been a target."
