That followed an investigation sparked by calls early this year to the ministry's 24-hour exotic pest and disease hotline (0800-809966) reporting deformed, watery and smaller-than-normal scallops.
One was from an Auckland recreational diver, Greg Hurt, who says all except one of 19 scallop beds off Gt Barrier's east coast from where he previously collected the delicacy have died out in the past five years.
As well as finding scallops in all three fisheries infected with Perkinsus Olseni, which is not considered a significant cause of disease in otherwise healthy animals, the ministry has acknowledged concern about inflammation and degeneration of the digestive tracts of some of the shellfish tested.
"This digestive tract damage is found in samples from all three sites and is the most significant finding in the investigation," Mr Gould said.
Regardless of the causes, into which there had been little scientific research, such damage reduced the ability of scallops to cope with other stresses.
Although Perkinsus Olseni was first suspected in New Zealand waters in 1999, its presence was mainly confined to clams and it was not found in scallops until late last year, at the top of the South Island.
But Mr Gould said all the diseases identified in the infected scallops were endemic to New Zealand, and there had been no breach of border controls.
Although the ministry has asked commercial fishers to notify it of anything unusual or suspicious, he said it was unlikely there were any actions they could take to guard stocks from parasites and disease in the marine environment.
Whangamata Seafoods co-owner Peter Sopp, whose seven-strong fleet of scallop boats is being prepared for a new harvesting season, did not want to comment until consulting other industry parties.
But an industry source suggested Perkinsus Olseni may have been present in scallop beds off the Coromandel east coast for many years, with little impact on the fishery.
The ministry estimates an annual retail value of almost $2.8 million from the Coromandel scallop quota management area, which extends from Little Barrier Island to Motiti Island in the Bay of Plenty.
It says an average of 46 tonnes of scallop meatweight has been harvested annually from the fishery over the past five years.