Scottish fishing leaders claim the European Commission's proposals to reform the Common Fisheries Policy will lead to big cuts to the fleet and jobs.
The EU wants to end over-fishing and the dumping of fish at sea, with skippers obliged to land all the fish they catch.
The Scottish Fishermen's Federation said the changes could mean a 20% cut in the Scottish fleet.
SFF chief executive Bertie Armstrong said more than 1,000 jobs could go.
The European Commission unveiled major plans to reform the EU's fishing industry and to stop catches being wasted.
The proposal, due to take effect from 2013, would give fleets quota shares guaranteed for at least 15 years.
"Discards" would be phased out - the practice whereby up to half the catch of some fish is thrown back into the sea to avoid going above the quota.
The CFP has been in effect for 28 years, but Maritime and Fisheries Commissioner Maria Damanaki said it had been a failure.
She said: "There is over fishing; we have 75% over fishing of our stocks and comparing ourselves to other countries we cannot be happy.
"So we have to change. Let me put it straight - we cannot afford business as usual any more because the stocks are really collapsing."
Mr Armstrong said there could be a reduction of about 400 vessels in the Scottish fleet.
Scottish Fisheries Secretary Richard Lochhead said: "There is a huge threat to Scotland lurking within these proposals because, alarmingly, the commission is advocating an expansion in the international trading of fishing quotas.
"Our fishing rights would end up with faceless overseas-based multi nationals, rather than in the hands of future generations of Scots fishermen.
"In the complex mixed-fishery of the North Sea it makes sense for Scotland and other nations to have more control over their own fisheries, working in partnership with neighbouring maritime nations."
There has been widespread public opposition to discards across the EU, with more than half a million people signing a petition publicised by UK celebrity chef Hugh Fearnley-Whittingstall.