Scotland’s fishing fleets face cuts to valuable fisheries such as cod and haddock under the Brexit deal negotiated by the UK, the Scottish government believes.

It said its analysis showed there would be increases in the quota available for Scottish trawlers in only five of 13 fishing areas around or close to Scotland, with clear falls in several of the largest such as North Sea cod.

Fergus Ewing, the Scottish cabinet secretary for the rural economy, said that despite claims by the UK government that the deal would greatly increase the catch for domestic trawlers, many fleets and ports would experience adverse impacts. That was “deeply troubling”, he said.

“This is a terrible outcome for Scotland’s coastal communities. The small gains in quota for mackerel and herring are far outweighed by the impact of losses of haddock, cod and saithe [coley] – and that threatens to harm onshore jobs and businesses too linked to harbours, fish markets and processing facilities.”

However, a senior member of the UK negotiating team said they “don’t recognise” the Scottish government figures, adding that overall the deal would benefit Scotland’s fish processing, salmon farming and seafood industry as a whole, as well as deep sea fleets.

He said winning a free trade deal meant there would be no tariffs or quotas imposed on any UK fisheries and seafood exports into the EU; by contrast Norway, which also has substantial fisheries and seafood exports, pays tariffs on its sales to the EU.

The UK government had also negotiated increases in the quotas requested by Scottish ministers over the five and a half year adjustment period which ends in 2025, including blue whiting, North Sea Angler fish, megrim and west of Scotland saithe, the source said, adding that the UK’s substantial North Sea herring quota had increased 10%.

He said the UK had to recognise that in striking a free trade deal, the impact of any cuts in quota for EU fleets had to be considered to ensure both sides interests were addressed.

“It’s absolutely clear that the deal we have done will deliver huge value to Scottish fishers over the transition and beyond,” the source said.

The Scottish government analysis found that in six fisheries, the percentage of the quota available to UK fleets during the adjustment period would fall, particularly for the most heavily fished species of cod, haddock and whiting.

Those quotas include North Sea cod, one of the most valuable white fish fisheries, which would fall from 63.5% to 57% for the UK. North Sea haddock, another valuable fishery, would fall from 92.5% of the quota to 84.2%.

The Scottish government analysis, which did not include financial or tonnage data, said the quota would increase in five fisheries, including Irish Sea and west of Scotland haddock. UK government data show those fisheries are about two-thirds smaller than their North Sea equivalents. It would remain static in two fisheries.

Ewing said the fine detail of the deal showed many of the apparent gains were either unrealisable because they were technical, or irrelevant because EU fleets were not catching their full quota allocation. The deal also meant UK fleets could not swap quota with EU fleets.

“The quota either being given up by the EU or negotiated as a win by the UK government is of no worth nor value to Scottish fishing interests,” Ewing said.

Mike Park, the chief executive of the Scottish White Fish Producers Association, said his members were “deeply aggrieved” about the immediate future. It was far from clear whether fleets would benefit greatly once the transition period was over.

“The issue of sovereignty and our future ability to negotiate additional shares after the five-and-a-half-year window would seem clouded by so much complexity that it is difficult at this time to see how the UK government can use its newly recovered sovereignty to improve the situation of my members,” he said.

The National Federation of Fishermen’s Organisations has condemned the deal as Boris Johnson’s “Ted Heath” moment, in reference to the then prime minister’s capitulation to the founding members of the European Community’s demand for access to British waters.

They say the UK team has jettisoned their interests and the deal does not stop French, Spanish trawlers fishing within six miles of the UK’s coastline.

The negotiating team denied this, saying the UK had regained sovereign control of British waters, albeit after a transition period, and this was “the diametric opposite of what happened in 1973”.