Giving evidence before a jury in the High Court at Wellington today, Stephenson spoke of his shock when he first saw the statement.
"I was furious, and frankly I still am."
He said journalists were not in the business of being popular and he expected criticism - but General Jones had not not attacked him on the issue, but on "something completely irrelevant".
"He played the man, not the ball."
Stephenson said the NZDF sent the statement to one of the most extensive news media distribution lists he had ever seen, including both major television channels and all the major newspapers and radio stations.
His lawyer Davey Salmon asked him if any news outlets had been left out, to which Stephenson replied: "None that comes to mind. Even I'm on the list."
Stephenson said he knew many of the reporters on the list, some of whom were senior journalists and others who were "very close friends".
He said he immediately started getting calls about the statement, and the blood rushed to his face with the shock.
"The phone just started ringing, person after person wanting a statement, wanting a comment," he said.
"I just had a sense of intense confusion and anger. I was just perplexed, I couldn't understand."
Many media outlets wrote stories using the statement or published it in full, he said.
Asked how the accusation had affected him, Stephenson said being fair, accurate and professional was at the heart of journalism.
"But to make stuff up, you don't do that, and all my colleagues sitting here will tell you that a journalist who fabricates information gets shown the door - no ifs, no buts. You don't do it."
The jury was this morning played an audio recording of a voice memo Stephenson dictated following his visit to the CRU base.
Stephenson told the jury he made "extensive" notes about the meeting when he returned to Kabul with his translator and driver, in addition to his initial notes during the meeting.
He then made a voice memo based on the notes and other observations from the base about 3am.
Stephenson said he then destroyed the second set of notes and stored the voice memo on his laptop using encryption.
In the recording, Stephenson said he initially went to the CRU base on April 25 but was denied entry.
He could see both the Afghan and New Zealand flags flying within the base.
The next day he returned and was "more successful". He was allowed entry to the CRU base, where he met with the commander.
He described the room where they met, which was lit with fluorescent lights and had a low ceiling.
Stephenson said he and the commander had discussed the role and reputation of the New Zealand troops, including the transfer of detainees to Afghan authorities.
General Jones sat within the courtroom, while investigative reporter Nicky Hager sat in support of Stephenson in the court's public gallery.
The trial continues.
