As part of the SNP's agreement with the Scottish Greens, the Scottish Government launched a consultation on designating Highly Protected Marine Areas (HPMAs), which closes today.
This would see at least 10 per cent of coastal waters around Scotland closed to human activity, imposing an extra barrier on aquaculture expansion, which is already highly regulated.
Salmon Scotland has warned HPMAs could put jobs in fragile coastal communities at risk and undermine the government's vision of a 'blue economy'.
The trade body's chief executive Tavish Scott said the plans appear to be driven by political agendas rather than science.
There is currently no evidence that the proposed HPMAs will work, Salmon Scotland said.
It urged the Scottish Government to undertake a thorough independent review of how science has been used to establish the policy framework and to consider all pressures on the marine environment in a balanced way.
Responsible stewardship of a healthy marine environment is vitally important for the sector.
One in three salmon farms already operate responsibly in marine protected areas (MPAs), which cover 37 per cent of Scottish waters.
Many of these MPAs were designated after the farms had already been established in the area.
Scottish salmon farms directly employ 2,500 people and support more than 3,600 suppliers, with a further 10,000 jobs in every Scottish Parliament constituency dependent on farm-raised salmon.
The sector adds £760million-a-year to the country's economy (GVA), and Scottish salmon is the UK's biggest food export.
Tavish Scott, chief executive of Salmon Scotland, said:
"We support proposals that can improve Scotland's marine environment. Scotland's reputation for the very best farm-raised and wild-caught seafood depends on the seas around our coastline. However banning responsible sea use is not the answer.
"Salmon farms occupy a tiny proportion of Scotland's waters, yet ours is one of the most important sectors of the marine economy and one of the biggest employers in the Highlands and islands.
"We have grave concerns that HPMAs as currently proposed will result in significant job losses in some of our most fragile coastal communities, and damage the Scottish Government's own blue economy approach that supports sustainable economic growth.
"If government proposals force salmon farmers out of marine areas, business will lose confidence in Scotland and turn their attention to our Scandinavian competitors. That means Scotland losing out on good, well paid jobs and investment when we need it most.
"There appears virtually no scientific justification about what HPMAs are intended to achieve. Nor is there any evidence that aquaculture cannot coexist within HPMAs as we already do with marine protected areas.
"Sustainable growth of the Scottish salmon sector is crucial for coastal communities, where the local salmon farm is often at the heart of the community and the main employer, as well as for the wider economy and the Scottish Government's vision for the country.
"HMPAs have been developed in isolation and jar with existing government policies such as the national marine plan, the aquaculture vision, trade and economic policy, economic policy and local authority development plans for the marine area.
"We urge joined-up policy making from the Scottish Government. Government should prioritise evidence-based policies that protect both the environment and the livelihoods of hardworking Scots.
"HPMAs appear to be politically driven, aimed at keeping the Greens on side rather than any real attempt to improve the health of our seas."
Click here to read Salmon Scotland's Consultation Response to the Scottish Government's HPMA proposal.