Defence Minister Gerry Brownlee says the New Zealand Defence Force's failed legal battle against journalist Jon Stephenson, which has cost more than $1 million and left a key witness seeking refuge in New Zealand, is "somewhat unsatisfactory".

The Herald revealed today that an Afghan police commander, whose evidence did not survive scrutiny in Stephenson's defamation trial, had not returned to Afghanistan after the case was settled and was now seeking asylum in New Zealand.

Mr Brownlee refused to comment on the specifics of the matter today, citing a confidential agreement the Defence Force signed when it made an out-of-court settlement with Mr Stephenson in December 2014.

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"The whole situation seems somewhat unsatisfactory, but I can't make further comment as a confidential settlement was reached with Mr Stephenson, and I don't wish to breach his rights," he said.

The minister was asked 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.

He referred further questions to the Defence Force but warned that they would not be able to "add a great deal" because of legal privilege.

Stephenson sued the NZDF 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.After its publication, Prime Minister John Key questioned Stephenson's credibility.

"I've got no reason for NZDF to be lying, and I've found [Stephenson] myself personally not to be credible," he said.

Mr Key stood by those comments today, but did not go into detail: "I've got my own experiences and I'll keep them to myself."

He said it would be "concerning" if the Afghan commander used the trial as a means of resettling in New Zealand, but added: "You'll have to take it up with the minister."