Europe's fishing chief called for a cut of up to 50% in next year's haul of cod reviewing evidence that the species is not recovering from being over-fished.
Scotland, where annual fishing revenues are around £445 million, looked likely to be hit hardest by the proposal from EU fisheries commissioner Maria Damanaki.
But fishermen said the science had been clouded by profound changes in the environment and needed reviewing.
Ms Damanaki's demand is likely to be modified by EU fisheries ministers, who have in the past backed fishermen, who have tended to back short-term profit over long-term sustainability.
She said cod stocks to the west of Scotland, in the Irish Sea and in the straits between Sweden and Denmark were showing no signs of being replenished and needed protecting.
Fishermen should halve their haul of cod from those seas in 2011, and cod catches from the Bay of Biscay and off Portugal's coast should be reduced by 15%, under the proposal.
Ms Damanaki proposed an increase in quotas for better-managed species, such as sole, hake and herring.
The science was disputed by Iain MacSween, chief executive of the Scottish Fishermen's Organisation.
He said there are huge changes in the marine environment - in temperatures, currents and tides - and fish are appearing in places they've never appeared before.