New Zealand's then-defence minister Wayne Mapp raised concerns about the treatment of detainees in Afghanistan during a visit there in 2010, an inquiry has been told.
The inquiry into the activities of New Zealand SAS troops in Afghanistan, as detailed in the book Hit & Run, this morning heard from the Ministry of Foreign Affairs, the New Zealand Defence Force and their lawyer.
Authors Nicky Hager and Jon Stephenson claimed in their book that a Taliban fighter was caught by the SAS, beaten then handed over to Afghan authorities and tortured.
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, headed by Sir Terence Arnold and Sir Geoffrey Palmer, that 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 with a unit of the Afghan National Police called the Crisis Response Unit (CRU). It was typically involved in rapid response and authorised to apprehend anyone believed to be involved in actual or imminent attacks.
Mapp, who was defence minister at the time, raised New Zealand's concerns with historic abuses committed by Afghan authorities and sought assurances of the human treatment of detainees apprehended by the Afghan National Security Forces, especially when working with the New Zealand SAS.
Mapp reiterated those concerns during a visit in August 2010 and sought further assurances.
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 to Afghan authorities, saying if it was true it would be concerning.
He asked Ferris to comment on it and insisted when she said she was reluctant to comment on facts that hadn't been established and was a scenario.
She reiterated that New Zealand forces had no ability to interfere with an Afghan criminal investigation or judicial process.
Hager, Mapp and a lawyer for Stephenson will speak to the inquiry today.