Mr Lochhead called on the commission to adopt a consistent approach when it comes to applying scientific advice, not to pick and choose when to follow science.
The Cabinet Secretary was commenting on the EC proposals for 2012 fishing opportunities for stocks not subject to international negotiations which have just been published.
Mr Lochhead said: "We're committed to safeguarding our valuable fish stocks and helping them to recover. Following scientific advice is vital if we are to achieve this."
"It is a great relief to see the first signs of recovery of the West of Scotland haddock stock. Seeing the haddock stock recover to sustainable levels should be a cause for celebration yet the proposals announced today will only punish the fishermen who have worked so hard on conservation."
"Despite scientific advice recommending a 410 per cent increase for the West Coast haddock Total Allowable Catch, the commission have only proposed a meagre 25 per cent increase. Not only does this penalise our fishermen unnecessarily it could also lead to an increase in discarded fish - something both we and the commission have been working hard to reduce."
"No one can imagine that the commission, if faced with evidence suggesting a 410 per cent cut would enforce a 25 per cent cut. There seems to be one rule for suggesting decreases in allocations, and another for increases."
"The evidence shows that the haddock stock can now support a targeted fishery, and the marked improvement in the state of the stock also means that the catch-composition rules are no longer appropriate for West of Scotland haddock and will only increase discards further."
"This flies in the face of the aims of both Scotland and the EU. We cannot talk about introducing discard bans whilst current discard-increasing measures remain in place. We will continue to work closely with the commission to ensure the urgent removal of these measures, but in addition are calling for the commission to urgently review and increase the proposed haddock quotas in line with the scientific advice."
"I am calling on the commission to adopt a consistent approach to implementing scientific advice to ensure a fair deal for our fishermen and continue the important stock conservation work which is already underway."
Also commenting on the proposal is Bertie Armstrong, chief executive of the Scottish Fishermens Federation.
We share with the European Commission the aims of sustainable food production from the sea. Unfortunately, this first set of proposals represents yet another huge missed opportunity by the European Commission," Mr Armstrong said.
"We had hoped that with the Scottish fleets record of discard reduction and stock conservation that a more intelligent approach to fisheries management would have been adopted by the EC this year. Unfortunately, we have another dose of the same old medicine."
SNP President Ian Hudghton MEP commented: "Just as the negotiations for reform of the CFP get under way, the Commission has served up a timely reminder of the total inadequacies of the current system. The Commission has ignored scientific advice and has made proposals which would see an increase in discards."
"The Commission has proposed a zero quota for cod off the Scottish west coast, in their words 'to stop fishing for cod'. A zero quota of course won't stop cod from being fished - it simply means that all cod caught will have to be discarded."
"Scotland's fishermen have worked hard to use innovative fishing techniques aimed at increased sustainability. These efforts have not been rewarded and instead the Commission are using the same old blunt and failed tools."
"These proposals merely highlight the failings of a centralised CFP - and increase the urgency for total reform and the return of real powers to Europe's fishing nations."
The Scottish white fish fleet have reduced discards of West of Scotland haddock by about a third between 2009 and 2010. The 2,808 tonnes of West of Scotland haddock estimated to have been thrown away by the Scottish fleet last year, worth an estimated 3.5 million, is more than the Commission are proposing for a Total Allowable Catch next year.
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