The Ministry for Primary Industries says it has nothing to hide about fishing industry monitor FishServe.

LISTEN ABOVE: MPI's Director of Fisheries Management Dave Turner speaks to Mike Hosking

Greenpeace has made a complaint to the Auditor-General about FishServe, the company contracted to monitor over-fishing, quotas and licences.

It says the company can't operate independently, because it's owned by Seafood New Zealand, the country's largest fishing industry lobby.

But MPI's Director of Fisheries Management Dave Turner told Mike Hosking FishServe has a limited role, which it's been doing well for almost 20 years.

"Their function is purely administrative - they collect data, enter it into a database and then pass this information to us for analysis."

He said Greenpeace is just boxing at shadows.

"This has been going on for just about 20 years and there are audits in place. We save taxpayers a considerable amount of money by using this approach."