A study carried out for the Scottish Government examined the impact of both the economic downturn and conservation measures on the fishing industry.
Environment and Rural Affairs Secretary Richard Lochhead said the research showed "just how economically fragile our fleets are".
He spoke after the study warned: "2009 is proving to be a difficult year for the UK fleet and profit levels are likely to be lower than in recent years."
The report found that low fish and fuel prices, along with restrictions on the number of days fishermen can spend at sea, were likely to have a major impact on profits this year.
And it warned a further reduction in effort in 2010 could lead to lower profit levels for the sector.
The study, carried out by economists at the industry body Seafish, said that in 2009 those boats fishing for cod, haddock and whiting were likely to see slightly lower operating profits than in 2007.
However it added boats in the prawn and langoustine sector were likely to see profits "significantly down" compared to 2007.
Scottish Government officials will discuss the findings when they meet European Commission officials later this month.
Mr Lochhead said: "Fishing is a tough way of life at the best of times, but this year the combined effect of the economic climate and the tough restrictions imposed by Europe has made life particularly difficult for our fishermen.
"We have stressed this point a number of times in our dealings with the European Commission and commissioned this study to provide robust evidence. It shows just how economically fragile our fleets are."
He added: "We are about to enter the annual round of autumn negotiations in Europe, when crucial decisions are taken on quotas and days at sea.
"This study will help inform our negotiating position and, as a first step, we will be discussing it with Commission officials later this month."
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