Former defence minister Wayne Mapp said he was aware of complaints by the New Zealand Defence Force about the treatment of Afghan detainees by US forces.
Mapp was giving evidence this morning at an inquiry into claims made by authors Nicky Hager and Jon Stephenson in their book Hit & Run about the activities of the SAS in Afghanistan.
Hager and Stephenson claimed in their book that a Taliban fighter was caught by the SAS, beaten then handed over to Afghan authorities and tortured.
"I was well aware that there had been abuses of detainees in the past by overseas militaries. In particular, I was aware of an incident where SAS soldiers had detained Afghan persons after a raid in Band e Timur in 2002. The detainees were handed over to US forces," Mapp told the inquiry.
"Subsequently, the NZDF complained about the way in which the detainees were treated by the Americans," Mapp said.
He also said he was aware that the treatment of detainees arrested by the Afghan police's Crisis Response Unit (CRU) where the SAS were involved could be problematic for the New Zealand Government.
"The reality ... was that the NZDF are only ever involved in these kinds of deployments when the host government and country has adequate standards in respect of human rights."
Mapp was responsible for the Cabinet paper which sought to redeploy the SAS to Afghanistan in 2009. The Rules of Engagement (ROE) were developed and attached to the Cabinet paper.
The ROE reflected the policing nature of the anticipated policing role of the New Zealanders. The SAS could use lethal force against the Taliban to defend themselves and others but only if they were actively hostile.
In the development of the ROE, Mapp made a distinction between Al Qaeda, the perpetrators of the September 11 attacks in the US, and the Taliban former government of Afghanistan.
As internationally declared terrorists, members of Al Qaeda could be killed rather than letting them escape.
But Mapp said the distinction became a moot issue given that in the two and a half years the SAS were deployed they were never tasked with capturing Al Qaeda members.
"On most occasions there was no actual combat. In fact, in over 90 per cent of missions, the SAS did not actually fire their weapons. Instead the Taliban were arrested by the CRU and dealt with through the Afghan justice system," Mapp said.
He said it was a high priority for him and for the Government to ensure that the NZDF complied with all relevant legal standards.
It had been for the previous Government also, with Mapp noting former defence minister Phil Goff had received assurances from the Afghan government that detainees handed over to its authorities would not be subjected to torture or capital punishment.
Mapp said that on joint operations between the SAS and the CRU, the detaining authority was the CRU, not the SAS.
"This did not mean the SAS would ignore what was occurring but it did mean that the primary responsibility for detainees rested with the CRU in almost all cases."
The SAS could not remove people from the custody of Afghan police or security forces or prevent an Afghan official from arresting an Afghan person.
His view, based on official advice, was that where the CRU detained a person, they were the responsibility of the CRU.
Mapp said his concern over detainee treatment continued and he monitored the issue closely, raising it at a number of levels.
He spoke to Amnesty International, International Security Assistance Force, Nato, other governments and the ICRC.
He also continued to raise the issue with his officials.
"Even where the SAS were not detaining individuals, I was concerned that New Zealand was taking reasonable steps to ascertain that persons detained by the CRU had their human rights respected."
Mapp said that to his knowledge, only one person was detained by the SAS, a mid-level Taliban commander in 2011.
He was handed over to US authorities before being taken before Afghan authorities. The man, named Musa Khan, was visited by an SAS medical officer and legal officer and was visited every month until he was handed to Afghan authorities.
In the middle of 2011, Mapp sought assurances from the NZDF about whether partnering with the CRU might render New Zealand complicit in torture.
Lieutenant General Rhys Jones responded that New Zealand must comply with international and domestic New Zealand law at all times.
"All evidence at our disposal suggests the CRU have acted appropriately in respect of persons that they have arrested."
He went on to say the "actions of our personnel in Afghanistan do not even approach the threshold for complicity [in torture]".
The inquiry this morning also heard from the Ministry of Foreign Affairs, the New Zealand Defence Force and their lawyer.
In MFAT's submission today, Heath Fisher, divisional manager international security and disarmament, said the NZDF did not detain and transfer any individuals directly to Afghan authorities.
The SAS detained only one person, a mid-level Taliban commander called Musa Khan, who was handed over to United States custody.
Fisher told the inquiry New Zealand operated under legal obligations prescribed by international law and that would apply to those detained by the NZDF.
However, if the prisoners were detained by Afghan forces during operations in which New Zealand took part, those legal obligations would not apply.
New Zealand forces in Kabul were partnered the CRU. It was typically involved in rapid response and authorised to apprehend anyone believed to be involved in actual or imminent attacks.
Fisher said New Zealand also negotiated its own detention and transfer arrangements with Afghanistan in addition to its other obligations in the event of direct transfers.
An agreement signed in 2009 included guaranteed access to visit and check the welfare of prisoners in Afghan custody by the NZDF, Red Cross and Afghanistan's independent Human Rights Commission.
A United Nations Assistance Mission in Afghanistan (UNAMA) report on Afghan detention facilities in 2011 highlighted widespread mistreatment of detainees, use of torture and a lack of access to legal representation.
This prompted New Zealand to stop transferring individuals to facilities named in the report or which had allegations of mistreatment or torture levelled against them.
The SAS was tasked in January 2011 with apprehending Musa Khan.
New Zealand did not operate any detention facilities in Afghanistan so Khan was transferred to the US operated Battlefield Detention Facility at Bagram Air Field.
Fisher said the US offered its standard conditions of transfer which were considered to be "broadly compliant" with New Zealand's obligations.
New Zealand diplomats and NZDF staff visited Khan and he was monitored by the New Zealand Government until he was brought before the Afghanistan Government's judicial authority.
Brigadier Lisa Ferris, director of Defence Legal Services, said that since 2009, only two individuals were directly detained by the NZDF.
One was Khan, the other was detained in 2012 by members of the New Zealand Provincial Reconstruction Team.
Both were transferred to US custody before being handed over to Afghan authorities.
Ferris said New Zealand forces had no authority to interfere with the conduct of any criminal investigation or judicial process.
Arnold said he and Palmer were troubled by the distinctions between apprehension by a foreign force or by Afghan authorities.
"Looking at it in a realistic sense, is it right to say that detention is effected only by the CRU and all the foreign force is doing is assisting that?"
Palmer quoted from Hit & Run on the arrest and handover by New Zealand forces of a detainee to Afghan authorities, saying if it was true it would be concerning.
Hager and a lawyer for Stephenson will also speak to the inquiry today.