Group spokesman Bob Meikle, of Akaroa, said the board felt the measures were unwarranted and unjustified, and the views of amateur fishers had been "totally disregarded" by the ministry.
The protection measures will ban set-netting to four nautical miles offshore along much of the South Island's east coast from October.
Mr Meikle said the board felt any goodwill from amateur fishers in co-operating with the ministry and Department of Conservation (Doc) had been "completely annihilated" and was worried any future input into fishing-related matters would be similarly disregarded.
The walk-out on representatives from the meeting at the ministries' office in Filleul St in Dunedin on Saturday should not be seen as board members acting like spoiled children not getting what they wanted, Mr Meikle said.
The board was made up of people who voluntarily gave their time to pass on the views of amateur fishers to the ministry and some had travelled from as far as Kaikoura to take part in the protest.
They were not against protecting endangered dolphins and less draconian measures introduced to protect Hector's dolphins at Banks Peninsula, including a ban on set-netting at times of the year when dolphins spent longer close to shore and not allowing nets to be set overnight, which had proven to work effectively, he said.
These measures, introduced in 1998, had reduced the rate of dolphin deaths from 24.8 a year to 0.2, he said.
"In our opinion that is totally acceptable."
The board had made a submission on proposals to introduce similar measures on the east coast of the South Island.
Ministry of Fisheries operations national manager Jonathan Peacey, who had travelled from Wellington for the meeting, said the relationship between ministry staff and the group had always been "very positive".
"I understand they feel very strongly about the issue and it will obviously have a major impact on recreational fishing."
However, it was always difficult to find a balance, he said.
"Their views are certainly taken in to account, but ultimately it did not go the way they wanted.
''At the same time, we have environmental groups saying the minister has not gone far enough and he should have restricted fishing even more to provide greater certainty to the long-term survival of dolphins."
