Officials at the EU are to examine the North Sea cod recovery plan.
The EU Fisheries Commissioner is to investigate stock levels
Skippers argue that global warming, not over-fishing, has been to blame for dwindling numbers and protested over December's 15% cod quota cut.
Fisheries Commissioner Joe Borg has now vowed to investigate how the plan can be made more effective.
Tory MEP Struan Stevenson said he had scientific evidence that North Sea cod had moved northwards because of an increase in sea temperature.
"No amount of draconian measures and savage regulations will cause an upturn in cod stocks," he added.
"Not until the North Sea cools down again can we expect to see any change in the situation, but by then we may have completely destroyed the Scottish white fish fleet."
Leader of the Scottish Fishermen's Federation, Bertie Armstrong, said: "There has been a strident cry from fishery representatives for this and we are delighted.
"If the main reason why cod recovery is not taking place is because of factors outside fishing then we stand in danger of crucifying the industry.
"Something is amiss with the current plan, it is not just due to over-fishing."
Scottish fishermen have been up in arms over the deal
A spokeswoman for the European Commission's fisheries and maritime affairs department said: "We are looking at how we can make the plan more effective and simplify some of the rules.
"Obviously the state of the cod stocks is still quite dire but we may be able to propose higher fishing possibilities depending on the scientific evidence."
The International Council for the Exploration of the Sea (Ices) had recommended the closure of the worst-hit fishing grounds in the North Sea.
The conservation group, WWF Scotland, said it made no sense to continue to allow targeted fishing on North Sea cod when it was on the brink of collapse.