"The investigation involves activity throughout the commercial supply chain; catching, landing, processing and exporting," Mr Baigent said.
Nine fishing boats and all aspects of processing were being investigated after the ministry received "varying indicators that there were issues".
He said inquiries during the past six months appeared to indicate large discrepancies between the company's catch records and export documents - where it alleged more fresh fish were exported than reported as caught - during an 18-month period.
The claimed discrepancy was expected to grow with the inclusion of domestic sales following investigations with associated entities, he said.
The business was the only one being investigated and no vessels had been seized so far.
Charges were not imminent, with the investigation expected to take several months.
"It will take some time yet to complete the investigation and no consideration of charges will be made until that is concluded," Mr Baigent said.
If proven, the behaviour undermined the Quota Management System, put the fishery at risk and made it more difficult for legitimate fishers, he said.
Staff in white gumboots loitered near the Pandora factory yesterday morning after being told to go home for the day, following interviews on factory production practices.
Mr Baigent said sending staff home was a company decision. "We certainly haven't put any imposition on them and are trying to work with the company to allow that product to be processed."
Most investigative staff were expected to return to their bases in other parts of New Zealand "but there will be a core group carrying forward the investigation", Mr Baigent said.
The company's retail shop remained open for business yesterday and construction continued on the company's new Pandora Rd office and factory.
The family has owned the site, including a corner-site fish shop and a service station, for more than 18 years.
The $3million expansion was expected to bring staff numbers to almost 200, with some based across the road on the former Firman Marine site.
The company is a quota owner, vessel operator, processor, wholesaler, exporter and retailer.
Science and Innovation Minister Steven Joyce toured company operations during an election campaign visit this month.
