The letter writer, who retracted the letter a day after sending it, said her complaint about taking undersized rock lobsters had nothing to do with marine reserves and it had been based on bad information.
Otago Rock Lobster Industry Association chief executive Chanel Gardner wrote to the Ministry for Primary Industries and the university on Monday to say "a member of the public", aboard a university research vessel, had been seen taking undersized crayfish from research sample pots during crayfish sampling operations.
Ms Gardner also supplied the letter to the Otago Daily Times.
In it, the person at the centre of the allegations was identified as a member of a local customary fishery management committee.
Their alleged actions raised questions about compliance with regulations, and the risk posed to the sustainability of the local marine ecosystem, Ms Gardner said.
"If there is a customary permit involved which justifies [the person’s] removal of undersized animals as opposed to the return of the stock, who issued it and is this common practice?" she asked.
The following day she wrote back to retract the letter and put an end to any ministry investigation it had started.
"The sources we were informed by had timeframes and important specifics wrong.
"At the time of writing, the letter was an accurate record of our concerns, but this morning new information came to light that removes the concerns," she said.
The person identified in the letter referred comment to Ngai Tahu, which was approached but declined to respond.
An MPI spokesman said since the letter had been retracted, the ministry had no comment to offer.
A university spokeswoman also said the university had no comment.
However, aquaculture and fisheries programme director Prof Chris Hepburn expressed incredulity.
Quite often university researchers used a customary authorisation within customary fisheries areas, he said.
They also had a special permit, which allowed researchers to take a certain amount of crayfish.
Crayfish were typically released and he expected the numbers of animals killed would measure "in the kilos", rather than the tonnes taken by the fishing industry.
"What we’re doing is research on climate change impacts on crayfisheries, for the industry.
"And this is — it’s absurd — and it’s almost like they want to go to war about these marine reserves."
Prof Hepburn, who was on the multi-stakeholder forum that recommended the marine reserves network be approved last year, noted that days before writing the letter Ms Gardner launched an online petition to reconsider the reserves and had raised concerns this summer.
The petition raises very similar issues to those in her complaint letter, fears that mana whenua will be allowed to fish the marine reserves with no legal sizes.
Largely, the points of view put forward had already been litigated for years, Prof Hepburn said.
"You would think the whole coast had been taken.
"I am just flabbergasted about some of the nonsense that’s been coming through.
"Really, we’ve been trying to work with the crayfish industry over the last five years, and we have been working really well with them, and I don’t understand where this is coming from."
Ms Gardner said there was no mention of marine reserves in her letter, and it and the ongoing campaign to re-think Dunedin’s marine reserves "cannot be tied together".
Nevertheless, people still had a chance to tell the government they did not want marine reserves, she said.
"Despite what has been said in the media, there are still some key steps that need to be taken by the government to implement.
"It’s just simply not safe shutting down from St Clair right up the peninsula."
Earlier this year, Department of Conservation regulatory strategy and design senior manager Anna Cameron said the next steps, before the marine reserve’s new rules took effect, would be completed mid-year.
