New Zealand soldiers helped collect biometric data for a controversial programme the public was never told about.

The revelation comes in the Stuff Circuit documentary series The Valley, which exposes that New Zealand soldiers were involved in the intelligence-gathering programme that the public never knew about. It involved going into villages with a handheld device, taking eye scans and recording fingerprints.

A former top intelligence official in Kabul said the device the New Zealanders were using was one called "Seek", and that the data was uploaded to ISAF, the International Security Assistance Force, which New Zealand forces in Afghanistan operated under, but then shared with the CIA.

Former Chief of Defence Retired Lieutenant General Rhys Jones admitted New Zealand soldiers were involved in the programme throughout their deployment to Afghanistan, but said, "It wasn't a secret. It was probably just [one] of the things we did we weren't told back here in New Zealand".

Though Jones maintains the programme wasn't a secret, there has been no reporting of it in New Zealand, and a search of Parliamentary records revealed just two obscure references to the use of biometric equipment by the New Zealand Defence Force, and neither were in relation to operations in Afghanistan.

Even a former Minister of Defence, Wayne Mapp, said he did not know about the programme.

Jones justified the biometric data collection as being integral for identifying known or suspected insurgents.

"This was a zone that was insecure, we needed to track people. It was almost… 'martial law', but the rules of the country at the time were that this is necessary for the Afghan police to know who's in the area".

Jones said New Zealand soldiers were focused on males aged 15-70 - the group known as 'fighting age males' - and admitted that they also scanned dead people, "to find out who they were, to be able to match that database, so who is this person that's been killed in a firefight and was carrying a weapon, or was around an IED site? Do we have information on them already?"

In Afghanistan, Stuff Circuit spoke to a former New Zealand patrol commander who also defended the use of biometric data collection, although conceded it was a tough question.

"It's a useful tool in terms of sorting out who may have involved in incidents and who's not involved".

However a former Afghan parliamentarian, Moeen Marastial, questioned New Zealand's role in the controversial programme, saying "Why are they taking bio data from me if I am innocent?"

He said Afghans knew the New Zealand soldiers' role in Afghanistan was as part of a Provincial Reconstruction Team. "They are in Afghanistan for reconstruction, for rebuilding, working for the roads, working for the schools, working for the hospitals. That's why it will be questionable to the people of Afghanistan. Taking biometric data is not reconstruction in Afghanistan."

Mapp, who was Minister of Defence from 2008-2011, told Stuff Circuit he did not know our soldiers were involved in the programme, but he too defended it, saying, "I'm not entirely surprised either because I suspect they were doing that of people that they might have felt there was a degree of risk and they need to be able to track them and put them in the database."

He said questioning New Zealand's involvement in the programme was "frankly naive, because obviously ISAF have to know about the insurgency."

- Stuff Circuit