The Defence Force says an article claiming that the SAS has handed prisoners to Afghan authorities, putting them at risk of torture, is factually inaccurate.
The story in Metro magazine in April suggested the SAS had played a key role in arresting and transferring prisoners to Afghan authorities in 2010.
The journalist who wrote the story, Jon Stephenson said he had spoken to an SAS soldier who captured an insurgent last year and handed him over to the Afghan National Army.
Under international conventions, New Zealand cannot transfer prisoners to countries where they might be subject to torture.
The Defence Force Chief, Lieutenant General Rhys Jones, released a statement on Monday rejecting the article.
Lieutenant General Jones says the implication that the SAS would hand over prisoners knowing they would be tortured is abhorrent.
He says, unlike the article claims, no detainees were taken by the SAS or anybody else in the so-called Tiger raid.
Lieutenant General Rhys Jones says another operation mentioned never happened.
He insists Defence Force processes are legally and morally sound.
The former chief of the Defence Force, Lieutenant-General Jerry Mateparae has also assured the Government the SAS has not handed prisoners over to Afghan authorities.
Call for inquiry
Earlier on Monday, Labour Party leader Phil Goff called for an independent inquiry into the reports the SAS had put prisoners at risk of torture.
He said he has a lot of respect for General Mateparae - who was Defence Force chief at the time - but before he becomes Governor-General in September there should be an independent inquiry.
But Defence Minister Wayne Mapp has rejected the call, saying the allegations have been investigated and proven to be false.