The Herald understands the person who returned to Kabul was an interpreter and that the commander remains in New Zealand and is pursuing an application to be accepted as a refugee.
It is unlawful under the Immigration Act to deport a person until their refugee application has been determined.
The Defence Force abruptly changed tack in its defamation case against journalist Jon Stephenson after the commander testified at a secret High Court sitting in Wellington on December 2014.
According to the court list, the hearing was "to take evidence".
After the hearing, the Defence Force settled with Stephenson, paid him a six-figure sum and expressed "regret".
During the three-year battle, the Defence Force used 15 lawyers at a cost of $643,000.
Stephenson sued the Defence Force chief at the time, Lieutenant General Rhys Jones, and the force, claiming he was defamed in a press release General Jones issued in 2011 in response to a Metro magazine article by Stephenson about the handling of detainees in Afghanistan. The article raised whether SAS troops had passed prisoners to authorities known to torture.
The journalist argued the press release accused him of making up a visit to an Afghan police Crisis Response Unit base in Kabul and interview with the commander.
The commander did not give evidence at a trial in July 2013 during the course of which, and in response to testimony by the journalist, General Jones accepted Stephenson had gone to the base and probably spoken to the commander.
Despite the judge directing the jury that there was now no challenge to Stephenson's account, the jury did not reach a verdict.
The Defence Force proceeded towards a retrial but in a statement last November said it and General Jones now accepted Stephenson did in fact gain entry to the base and interview the CRU commander.
The Defence Force paid for the commander to fly to New Zealand on November 10, 2014.
The secret hearing was in early December and he was booked to fly back to Kabul on December 15 but did not board the flight, a Defence Force spokeswoman confirmed.
The spokeswoman said the Defence Force had not offered support for the commander's immigration application.
No explanation was given for abandoning the planned retrial.
That was "subject to legal privilege", the spokeswoman said.
No response was received in time for this report about whether the Defence Force had asked the commander to provide evidence by sworn affidavit or video link from Kabul instead of travelling to New Zealand.
Prime Minister John Key attacked Stephenson's credibility at the time.
"I've got no reason for the NZDF to be lying, and I've found [Stephenson] myself personally not to be credible," Mr Key said in May 2011.
Mr Key's office last night said the Prime Minister had nothing further to add.
Defence Minister Gerry Brownlee did not respond to questions in time for this report, including whether he was happy with the way the matter had played out, whether there would be an inquiry and whether the Immigration Service would be informed that the commander's evidence appeared not to have stood up to scrutiny.
Stephenson said there were several matters relating to his case that were still before the court.
"My legal advice is not to make any comment that might prejudice those matters."
Green Party defence spokesman Kennedy Graham said the NZDF's defamation case had become "something of a shambles".
The public had now stumped up $1 million for a court case "that should never have happened in the first place", he said.
Dr Graham said he was not opposed to the Defence Force's decision to fly the Afghan commander to New Zealand to testify in the case.
"But what's not appropriate is that the whole trial erodes from the attacking of the personal credibility of a very well-reputed New Zealand journalist.
"And that is a pattern of behaviour that the Prime Minister has led this Government on, including the Nicky Hager issue in late 2014."
Stephenson's Metro article, "Eyes Wide Shut: The Government's Guilty Secrets in Afghanistan", won the international journalism award the Bayeux-Calvados Prize for War Correspondents and the top investigative award at the 2012 New Zealand Canon Media Awards.
In the article, Stephenson said the CRU commander told him New Zealand's SAS was "very, very involved" in detaining suspected insurgents.
An internal email from a top Defence Force colonel, tabled at the defamation trial, suggested a statement denying Stephenson interviewed the commander was needed to damage the journalist's credibility and stop an inquiry into revelations he made.
The email, from Colonel Jim Blackwell to other senior Defence Force staff, read: "Get a signed and witnessed statement by [the commander] that he has not done an interview with Stephenson.
"The more that we can prove that his [Stephenson's] statements continue to be false, then the earlier that we can stop parties requesting an enquiry ..."
Colonel Blackwell, who previously commanded the elite SAS group, left the military in July 2015 after 31 years of service.
Lieutenant General Tim Keating replaced General Jones, who left the Defence Force after a 35-year career, in January 2014.
General Keating is a former head of the army and also commanded the SAS.
How the story unfolded
Following news last year the Defence Force had settled a three-year defamation case with war reporter Jon Stephenson, the Herald began to seek information under the Official Information Act.
In October, the Defence Force disclosed it used 15 lawyers at a cost of $643,000. This was in addition to a six-figure settlement payment made to Mr Stephenson.
In November, it disclosed $23,466 was spent on flights and $25,871 spent on "interpreter expenses".
In February, it disclosed two people were "booked" to fly from Kabul to Wellington on November 10, 2014, and to return to Kabul on December 15, 2014.
The Herald noted the response said "booked" and asked for confirmation both people departed.
On February 15 this year, the Defence Force responded: "One of the two people flights were booked for returned to Afghanistan after the trial, while the second did not board their flight. No further information is able to be provided on the second person."
Herald inquiries indicated that the person who did not leave is the commander and he is seeking to remain in New Zealand as a refugee.
The Defence Force last week said it had not offered the witness from Kabul support for his immigration application.
As to why it changed tack and chose to settle after so long, it said: "NZDF has no comment to make except to say that the conduct of litigation is a matter subject to legal privilege."
The Herald is awaiting an answer as to whether the witness from Kabul was asked to provide evidence by way of sworn statement or video link as an alternative to travelling to New Zealand.
