Rules forcing skippers to dump some fish overboard have been criticised
Decision-making powers must be returned to Scotland before it is "too late" for fishing communities, ministers say.
The fisheries secretary is arguing for "regional" influence as part of wider reform of the Common Fisheries Policy that governs EU member states.
Richard Lochhead hopes to highlight the position as part of a debate on the policy's future being held in Brussels.
Micromanagement from Brussels had "bedevilled" the sector for decades, Conservative MEP Struan Stevenson said.
Mr Lochhead has joined the industry in criticising rules which force skippers to dump some fish overboard to meet quotas, a practice known as "discards".
He said: "Our guiding principle remains that decision-making must be returned to Scotland where it belongs.
"Within a regionalised framework there is much greater autonomy for fishing nations to balance the economic, conservation and social goals of fisheries policies.
"However, we cannot afford to wait for 2013 for radical changes, we need them now, before it's too late for our fishermen and fish stocks."
Mr Stevenson, who is also vice-president of the European Parliament's fisheries committee, said: "Micromanagement from Brussels has bedevilled our fisheries sector for decades.
"We have a chance to put things right."