The Ministry for Primary Industries made the decision to remove all farmed oysters from the bay in 2017, after Bonamia ostreae was detected on oyster farms in the area.
The invasive parasite kills oysters.
Since then, the ministry has been carrying out monitoring testing on wild oysters from the bay, and a technical advisory group and the Bonamia programme advisory group stated returning to flat oyster farming in Big Glory Bay would pose an unacceptable risk to the Bluff oyster fishery.
However, oyster farmer Richard Langdon was frustrated, and believed the ministry was not being truthful.
He believed it was "targeting" independent marine farmers and wanted to put an end to flat oyster farming on Stewart Island, he said.
"We don’t want to be forced out from the last [flat] oyster farm in New Zealand. If it closes, you will never get a permit for another one - ever.
"We tried to but were never part of their consultations. The big quota owners from Bluff took over the industry and excluded everybody else."
Since 2017, Mr Langdon had farmed in Horseshoe Bay, doing his own research and investing more than $500,000.
However, he had had enough and wanted to take his chances and return to Big Glory Bay.
He acknowledged it was a complex issue but said several incidents highlighted why he could not trust the ministry.
He claimed the ministry found the parasite in 2016 in Big Glory Bay but "covered it up".
The August 2016 report "Monitoring Bonamia ostreae in dredge oysters" stated that Niwa found six oysters with the disease - one in the Big Glory Bay area.
However, MPI stated it was "confident this result was a false positive due to cross-contamination", he said.
"The sample we're talking about is a full year before MPI found Bonamia ostreae in 2017 and farmers had lost any chance they had to react."
Mr Langdon then filed two requests under the Official Information Act about B. ostreae being found in Big Glory Bay, and both responses denied the parasite had been found there.
An idea of getting independent testing done, which he would pay for himself, met a dead end as there were only two bodies accredited to do it - Niwa and MPI.
He said the problem was highlighted when MPI established a technical group in 2019 to look at whether flat oyster farming posed a risk to wild oyster populations.
Mr Langdon said he met some scientists of this group who told him that they never heard about any positive or false positive in the area before 2017.
"They knew nothing about this positive [case] because it was kept from them. So they [MPI] are cherry picking the information they gave to these people and expect them to go and make a good decision?"
Mr Langdon said he had to wait "like an obedient child" while MPI carried on with its consultation on the future of flat oyster farming in New Zealand.
"We are quite happy to take our chances with our new and improved farming method, but we feel stuck at the moment."
Asked for comment, MPI denied Mr Langdon’s claims.
Biosecurity New Zealand pest management group manager John Sanson said the recommencement of oyster farming in Big Glory Bay was not possible, primarily due to the fact the area was infected with the parasite and flat oyster farming operations had the potential to proliferate and exacerbate the spread.
"It is worth noting that experience in other countries has shown that Bonamia ostreae has never been eradicated from a location once positive detections have been found."
Biosecurity New Zealand’s animal health laboratory (AHL) reached the conclusion that the results could have been false positives because its own follow-up testing of Niwa’s positive screening tests produced negative results that contradicted Niwa’s.
The contradictory results or potentially false positives could be the result of cross-contamination of samples.
"We understand that Niwa’s own assessments are that the risk of cross-contamination is very low, but that is not the view of Biosecurity New Zealand."
Mr Sanson said the agency had given the technical advisory group all reports on the matter.
"There is no evidence anywhere that Biosecurity New Zealand [the biosecurity arm of MPI] ‘wiped’ any information about the one positive oyster found at Big Glory Bay from its records.
"It is clearly stated in the executive summaries of both surveillance reports that the parasite was found in one oyster from Big Glory Bay. "
He vehemently denied any favouring of any part of the oyster industry by MPI; one of the Ministry’s priorities was to support innovation and partner with food and primary sectors for their success, he said.
"There has been a demonstrated ongoing commitment to supporting aquaculture - which includes oyster farming - to achieve its goals. Likewise, there is a focus on protecting the country from harmful pests and diseases, and in this case, that includes working to keep Bonamia ostreae out of the wild oyster fishery and marine farms.
"MPI and Biosecurity New Zealand have demonstrated complete transparency in its dealings with [Mr Langdon] and other parties involved in the management of Bonamia ostreae, which is a complex issue. "
