A report by the Royal Society of Edinburgh has called for Europe's national governments to take responsibility for fish stocks.
The report urges ministers to take action to save the fishing industry
It said fishermen and scientific experts had played a part in allowing cod stocks to collapse.
But the study criticised the Common Fisheries Policy (CFP) for failing to protect key fish species.
The report was welcomed by the Scottish Fisheries Minister Allan Wilson, who said it would inform future debate.
The independent study by leading marine scientists urged ministers to take action to help develop a more viable long term industry.
It said the European Union's CFP was too centralised and remote from those it affects.
Among a series of recommendations, it said responsibility for conservation should be returned to a national level.
It also called for the present system of catch quotas to be replaced by restrictions on where and how often vessels can fish.
Commenting on the findings, Mr Wilson said: "The launch of this inquiry last May by the Royal Society of Edinburgh was widely welcomed by industry and politicians alike.
"I hope these extremely well-researched and coherent findings will be just as well received."
Mr Wilson also promised that the report would inform future Scottish Executive policy on fishing.
He said: "Scottish ministers will certainly by giving these recommendations our fullest consideration."
Westminster fisheries minister Ben Bradshaw said the government would soon impose monitoring restrictions to make sure fishermen obeyed the new quotas.
His promise came on the back of new evidence suggesting illegal landings have shot up by 200% in parts of the UK on the back of the quotas.
"If we don't get to grips with that then it is not only bad for the stocks,
it is unfair on those fishermen that stick to the rules," he said.
"Since we have had to take some very painful decisions in relation to cod and other white fish stocks the temptation, or some in the industry might argue, the
necessity of economics have been to ignore the rules and catch and land illegally.
"The problem is if you carry on catching at the present levels then you will end up with a situation where there are no fish left to catch and fishermen will all be put out of business."
However, the Scottish Conservatives' fisheries spokesman Ted Brocklebank MSP described the report as "a Curate's Egg which defies the logic of its own findings".
He said it contained good, bad and "occasionally wrong-headed" analyses of the fishing industry.
"Perhaps the most important finding in the report - especially as it comes from a body of eminent scientists - is that the scientific evidence upon which the executive has made many of its most damaging
decisions for the Scottish industry is not as robust as ministers have claimed," he said.
"We totally agree that the industry must be more involved in future scientific assessments of stocks."