Four skippers, including at least two from Dunedin, are being investigated for refusing to take an observer on board during the Ministry of Fisheries Hector's dolphin programme.
The two-month national programme to assess the interaction between fishing vessels and dolphins ends this weekend.
Ministry of Fisheries national environment manager Steve Halley said the department was "actively investigating" those skippers as they were legally required to take an observer on board.
The ministry would not identify the skippers.
They face a possible fine of up to $250,000.
Port Chalmers Fishermen's Co-operative president Steve Little said he was being investigated and believed the others also being investigated were from Taieri Mouth and Bluff.
He was still waiting to hear back from the ministry regarding possible prosecution after having a formal interview with his lawyer present a few weeks ago.
In the past fortnight, his book-keeper had also been spoken to, he said.
"It's just wait and see."
Taieri Mouth fisherman Gary Homan confirmed he was being investigated as he refused to take an observer because he was only certified by Maritime New Zealand to carry two people on his boat.
"It meant we missed out on the most lucrative two months of fishing."
Mr Halley said the ministry would now review the programme in light of the issues raised to determine if, and how, any subsequent programmes might progress.
Members of the industry would be involved in those discussions so the issues could be resolved for any future programmes, he said.
"We're very keen to talk to them directly to understand the issues."
It was hoped a way to assess the interaction between dolphins and the fishermen could be found that did not "upset anyone", Mr Halley said.
It had not yet been decided if the programme would go ahead again.
The Labour government had provided extra funding for the ministry's observer programme, but it had not yet been decided how and where to use the funds.
"We need to review the inshore programme and talk to industry about that."
The programme had surpassed its target of 900 sea days, achieving 950 with observers going on board 47 vessels, he said.
They were still in the process of analysing the information from the programme, which recorded 800 sightings of Hector's dolphins.
"They saw a lot of dolphins, some in areas closed [to commercial fishing] and some not."
No dolphins were caught during the programme.
A detailed report would be produced in the next couple of weeks.
New Zealand Commercial Fishing Federation president Doug Sanders-Loder said it would be happy to be involved in a "robust" review of the programme.
"It's imperative the practitioners are involved in deciding the outcome for future programmes."
The fishermen who had refused to take observers were protesting on the basis of process, he said.
"It's about process, implementation; about cost."
There were also alternative ways the programme could be implemented which could be discussed, he said.
