The Cod Recovery Plan, agreed in Brussels in 2008, is a "legal straightjacket which threatens to cause yet more obscene waste in our seas", according to Richard Lochhead.
The European Commission has "stubbornly insisted on its rigid requirement" for more automatic cuts in days at sea for Scottish fishermen this year.
Despite an increase in cod stocks, the recovery plan's rigid rules also seeks to cut the amount of the fish that can be taken from the North Sea by 20% in 2013.
Cod numbers are steadily recovering, having more than doubled in the last six years, said Mr Lochhead as he addressed MSPs before crucial European fishing quota talks.
Scottish fishermen have made the greatest reduction in cod discards in Europe, he said.
He added: "We have got to move away from Brussels-based micromanagement and bring decision making closer to home, to those who best know our rich and diverse waters."