In outspoken responses to an official consultation, they have accused Scottish ministers of wanting to remove their 300-year-old right to fish, and of threatening the livelihoods of costal communities.
But some of their arguments have come under attack as being "very misleading" by a leading academic expert. And environmental groups have called on ministers to reject "short-sighted" fishing in breach of ecological limits.
Ministers are developing a national marine plan to enable the "sustainable economic growth" of fishing, renewable and other marine industries. But their approach has been angrily rejected by the Scottish Fishermen's Federation (SFF), in a submission posted online.
"Sea fishing, which has a tradition almost as long as the existence of the nation, deserves protection in the planning process in the same way as protection in the terrestrial planning process is granted to agriculture," it says.
"Unfortunately, the opposite is the case when it comes to be assessed against sustainable development. The additional twist of the screw is that fishermen will not receive any form of compensation for the loss of their livelihoods and the inevitable depression that that will bring to families and communities."
The SFF expresses "deep disappointment", claiming that fishing is being given a lower priority than marine renewables, like offshore wind farms.
The SFF submission suggests that the plan threatens the historic right to fish in Scottish waters, granted in legislation passed by a former Scottish Parliament in 1705.
Another submission, from the Clyde Fishermen's Association, warns that the marine renewables encouraged by the plan could damage the future of fishing.
The SFF's submission was criticised by Professor Murray Roberts, director of the Centre for Marine Biodiversity at Heriot-Watt University in Edinburgh. He said: "The SFF response rests on the erroneous assumption that agriculture and fishing are similar, though in fact they are fundamentally different.
"One uses the land to grow crops or farm animals, while the other relies on capturing wild animals from the marine environment. The analogy is stretched to breaking point when it's suggested that trawling the seabed is like ploughing a field.
"It is vitally important that the scientific evidence underpinning future sustainable fisheries is not misrepresented.''
Environmental groups already take ministers to task for not doing enough to ensure that marine wildlife will be protected.
Calum Duncan, from umbrella group Scottish Environment Link, which brings together over 30 groups, added: "Everyone wants a viable and healthy fishing industry, and introducing measures to reduce the environmental footprint of fishing activities will help the industry in the long-term."
Alex Kinninmonth, from the Scottish Wildlife Trust, argued that the draft plan distorted the concept of sustainable development.
"It fails to fully recognise that healthy seas and the protection of natural resources are a requirement for the long-term prosperity of the marine economy and coastal communities," he said.
The SFF denied it was attempting to derail the national marine plan, and expressed surprise at Roberts' "hostile" comments. "Any new plan must take account of existing and traditional rights, while explaining properly any change of regulation or approach," said the federation's chief executive, Bertie Armstrong.
A spokeswoman for the Scottish Government said there had been a diverse range of responses to the plan. She added: "The feedback we have had illustrates the difficult balancing act that has to be achieved, and that is why we will carefully consider all the consultation responses before a national marine plan is introduced."