Scotland’s most influential fishing lobby on Friday denounced Boris Johnson’s trade agreement with the EU as “desperately poor” and accused the UK prime minister of making deceptive claims about the post-Brexit deal that it said leaves the sector worse off in half its key whitefish stocks.

The strongly worded open letter from the Scottish Fishermen’s Federation — previously a vocal supporter of leaving the EU — will fuel accusations that Mr Johnson betrayed the industry’s interests to seal the deal.

But it could also seriously damage the Conservative party’s prospects in Scottish coastal constituencies just four months before the country’s parliamentary elections. The governing Scottish National party is well ahead in the polls and hopes a decisive win will pave the way for another independence referendum.

The Brexiters that predominantly make up the UK government since Mr Johnson led the Conservatives to a resounding win in the 2019 election, have long cited fishing as a sector that would benefit from leaving the EU. The issue helped Tory candidates win and defend seats in Scottish fishing communities in the 2017 and 2019 general elections.

The Scottish sector dominates the UK fishing industry, accounting for more than 70 per cent of landings of quota species.

Asked about the letter, Downing Street said the EU deal would bring “immediate gains” for fishermen and women across the UK.

“We have now taken back control of our waters and the agreement we have reached with the EU secures a 25 per cent transfer of quota from EU to UK vessels over five years,” it said.

The SFF specifically criticised the quota claim in its letter to the prime minister. “You and your government have spun a line about a 25 per cent uplift in quotas for the UK, but you know this is not true, and your deal does not deliver that,” wrote Elspeth Macdonald, SFF chief executive.

“Your deal actually leaves the Scottish industry in a worse position on more than half of the key [whitefish] stocks and now facing acute problems with North Sea cod and saithe in particular,” Ms Macdonald wrote.

The federation, which previously hailed Brexit as offering a “sea of opportunity”, warned the deal with the EU deal would cause long-term problems.

The first two weeks of post-Brexit transition trade in seafood products have been marred by widespread IT and paperwork problems that the SFF said had left many fishing vessels tied up in harbour and others forced to make 72-hour round trips to Denmark to land fish.

The row over the fishing deal came as another freight distributor announced it was suspending services to the EU from Saturday for at least a week, citing a backlog of consignments caused by incorrect customs paperwork.

In an email to customers Palletways, one of Europe’s largest networks collating and distributing individual pallets of goods, said that it could no longer accept orders. “No entry of Brexit consignments will work on the portal until January 25th,” the company said in an email seen by the Financial Times.

The suspension follows similar moves by DPD earlier this month, while this week DB Schenker suspended shipments from the EU to the UK. Both cited paperwork issues.

Rod McKenzie, director of policy at the Road Haulage Association, said the Palletways suspension was “a very significant blow” given the relatively low volumes of freight currently crossing the Channel due to pre-Christmas stockpiles. He urged the government to “take rapid action” to avoid the situation worsening next week.

Palletways UK did not immediately return a request for comment.

Anger in the fishing sector has been fuelled by the disruption and delay to shipments of live and fresh seafood to the EU, problems that industry groups said threatens the survival of smaller exporters.

The SFF demanded Mr Johnson urgently provide compensation for fishing businesses, insisting he ensured it was “new money” and was not taken from the £100m the UK government had already promised to invest in the sector.

Downing Street said it recognised that the Scottish fishing industry was facing “some temporary issues following the end of the transition period”. “We are looking at the additional financial support we can provide,” it said.

The Welsh government has also demanded compensation for its fishing sector.