London, Paris and Brussels were tonight at loggerheads in the first major trade dispute of the post-Brexit era, after Boris Johnson deployed gunships in the English Channel in response to the threat of a blockade of Jersey by French fishermen.

Violence was avoided but a Channel Island ferry was delayed by four hours as a flotilla of 56 French trawlers converged on St Helier port in scenes one local fisherman described as “like an invasion”. French maritime authorities in Cherbourg dispatched two police coastal patrol boats to “ensure the security of navigation and safeguard human life”.

Mr Johnson faced charges from Brussels of breaching the terms of the Trade and Cooperation Agreement (TCA) which he signed on Christmas Eve, through the imposition of additional conditions on EU fishing vessels operating in the island’s territorial waters.

EU law expert Professor Catherine Barnard, of Cambridge University, told The Independent the stand-off was likely to be the first of many confrontations over the implementation of Mr Johnson’s deal.

“This is the first sign that the TCA is being engaged and that we are under a new set of rules which are going to be enforced,” said Prof Barnard, deputy director of the UK in a Changing Europe think tank. “There have been disputes between fishermen before, but previously we were members of the EU and the European Commission could act as the honest broker.

“We’ve always known it was going to get choppy and that politics would get involved, particularly at a time when there are elections happening and the prime minister knows that what unites a lot of his voters is anti-EU sentiment, as well as regional elections coming up in that part of France.”

Fury among French fishermen was sparked by new licences issued to 41 boats by the UK’s Department for Environment, Food and Rural Affairs (Defra) on Friday, to come into effect the following day.

They complained that ships which had operated in the island’s waters for decades were being asked to provide proof of former presence there, and that they were being subjected to new restrictions on fishing days and hours and areas of operation.

Fishermen’s leader Dimitri Rogoff said boats from French ports all along the western Normandy coast had gathered to protest, but insisted they had never intended to blockade the port.

“This isn’t an act of war,” Rogoff said. “It’s an act of protest.”

Jersey fisherman Josh Dearing said it was “quite a sight” to witness the French mariners letting off flares and bangers as they gathered offshore from around 4.30am.

“It was impressive,” he said. “I looked from the shore this morning and it was just like a sea of red lights and flares already going off at sea. It was like an invasion.”

In the event, boats which entered the harbour succeeded in delaying the departure of the cargo vessel and ferry Commodore Goodwill. And they held 90 minutes of boat-to-boat talks with Jersey’s environment minister Gregory Guida, as one French and one Jersey vessel moored alongside one another.

Mr Johnson spoke by phone with chief minister John Le Fondre to reiterate his “unequivocal support” for the island and assure them that the offshore patrol vessels HMS Severn and HMS Tamar would remain in the area “to monitor the situation as a precautionary measure” while the tension remained.

In Paris, Europe minister Clement Beaune said that France “won’t be intimidated by these manoeuvres” and called for “a quick and full application of the deal” not only in the Channel Islands but also in relation to licences being awaited in the Hauts de France region around Calais and Boulogne.

Following the departure of the French flotilla, the UK gunships remained in post for some time, with one due to return to port on the mainland on Thursday evening and the other on Friday.

The European Commission appealed for “calm”, but demanded “full compliance” from the UK with the TCA’s requirements for any limits on fishing activities to be non-discriminatory, based on a clear scientific rationale and notified in advance to those affected.

“Until we have received further justifications from the UK authorities we consider that these new conditions should not apply,” said spokeswoman Vivian Loonela, who said commission officials were in talks with Defra.

A commission spokesperson refused to say whether France would be within its rights to retaliate by cutting off electricity supplies to the island, as one minister threatened earlier this week.

Prof Barnard said the TCA included a provision expressly ensuring that EU boats should have access to Jersey and Guernsey waters reflecting their activities over recent years. 

If France does not feel it is being treated fairly, it has the option of retaliating with “compensatory” measures, which could include withdrawal of access to its waters or tariffs on UK fish products. 

And the whole dispute could be escalated to an arbitration panel – made up of one UK and one EU member plus a chair agreed by both – for judgment, with the possibility that either side could step up its action by targeting other sections of the economy.

Prof Barnard said that an electricity blockade would almost certainly overstep the agreement’s stipulation that retaliatory action must be “proportionate”.

But she said Paris would have the option of “painful and politically difficult for the UK government”, such as imposing tariffs on seafood products from outside the Channel Islands, such as Scottish salmon.

Following the departure of the French boats, Mr Le Fondre said that Jersey was proposing the establishment of a new forum to take the heat out of the issue by enabling the island’s authorities to engage with all fishermen in the region “openly and constructively”.

But the head of the Jersey Fishermen’s Association, Don Thompson, said there would be “absolutely no further negotiation” with the French, who he blamed for creating the problem by failing to keep the records of historical catches which would allow boats to prove their right to fish.

“If the data that came from France is not accurate or not good, then French fishermen might not have received the full extent of their number of days or the type of fishing that they did,” he told Times Radio. “So they’ve been told today they need to go back and take this up with France with their own administration. It is a Franco-French problem.”

A UK government spokesperson said: “The Trade and Cooperation Agreement brought in changes to fishing arrangements between the UK and the EU. Jersey authorities have a right to regulate fisheries in their waters under this agreement and we support them in exercising those rights.

“We will work with Jersey to support the discussions underway with the European Commission.”