"I don't know if they realise what this means to the Scottish fishing industry. It will mean the total closure of our fisheries.
"This is at sea and onshore and it will be thousands of jobs."
The federation's secretary, Dr Ian Duncan, said Prime Minister Tony Blair should start negotiating on behalf of the UK.
Doug Beveridge, assistant chief executive of the National Federation of Fishermen's Organisations, added: "If the advice were to be adopted it would have a devastating impact on coastal industries and communities.
"The industry is concerned that the scientists are basing their advice on information about fish stocks which was gathered in 2000 - and projecting ahead for 2003.
"But, in the meantime, surveys by the fishing industry indicate that the decline in cod stocks has bottomed out.
"We believe an assessment needs to be made of the recovery programme measures which are already under way and have been for a while."
The Scottish National Party's Westminster leader, Alex Salmond, has called for an emergency statement in the Commons on proposals.
Scotland's Fisheries Minister Ross Finnie admitted that the proposals could have "hugely serious implications" for the industry.
He told BBC Radio Scotland: "I certainly accept that this is one of the most serious scientific reports on the state of the fishing industry that anyone has seen for a very long time."
However, the minister said there was some way to go before the final settlement on fishing arrangements and there was much still to be considered.
He said: "It's a very, very serious report on the state of certain stocks in the North Sea.
"I certainly want to take time to have from my own officials a very detailed analysis of what is a very complex report.
"Much more importantly, I want to be able to sit down with the fishing industry itself, before we come to any conclusions."
Mr Finnie said he had the "extraordinarily difficult job" of balancing fishing and stock considerations.
SNP leader John Swinney said: "Ross Finnie has to act now to prevent the legacy of the CFP (Common Fisheries Policy) being the destruction of the Scottish fishing industry.
"The EU review of fishing policy should be undertaken before any decision is made on the future of the white fish grounds and Ross Finnie has to now fight to ensure the future of the fleet and of fisherman's livelihoods."
Scottish Tory MEP Struan Stevenson said: "We are talking about the loss of 8,000 jobs and loss of £500m to the Scottish economy if this goes ahead."
Researchers from the International Council for the Exploration of the Seas (ICES) provide information on stock levels, which is used as the basis for EC fishing quotas every year.
Scottish fishermen have travelled to Strasbourg, where they will meet scientists on Thursday and hold talks with senior officials on Friday.