French and other EU fishing boats can expect to be boarded by the Royal Navy and maritime coastguard when in British waters and a process will be triggered that could lead to tariffs on the bloc’s exports if Paris acts on its recent threats, Brussels has been warned.

David Frost, the UK’s Brexit minister, hit out at the “unjustified” measures that the French government has said it will impose from next Tuesday over a row about fishing access, during a meeting with the EU commissioner, Maros Sefcovic.

Sefcovic was told that Downing Street would consider “launching dispute settlement proceedings” and subject all EU vessels to “rigorous enforcement processes and checks” when in British waters.

Fisheries protection is carried out by both the maritime and coastguard agency and Royal Navy river-class patrol vessels.

The warning from London followed the French government’s announcement earlier this week that it will from Tuesday impose heightened customs and health checks on British goods, potentially impose a ban on boats landing fish, and scrutinise UK vessels’ security, environmental standards and crew.

The measures, to be enforced at the ports of Cherbourg, Granville, Barneville-Carteret, Boulogne-sur-Mer, Le Havre and Brest, will only be lifted if the UK and Jersey provide more licences for French vessels seeking to fish in their coastal waters, French ministers have said.

France’s prime minister, Jean Castex, has written to Sefcovic notifying the commission of the government’s intentions, urging Brussels to support its plans. A commission spokesman said the measures were being examined to see if they were compliant with the EU-UK trade deal.

A UK government spokesman said Frost had set out “concerns about the unjustified measures announced by France earlier this week to disrupt UK fisheries and wider trade, to threaten energy supplies, and to block further cooperation between the UK and the EU, for example on the Horizon research programme”.

Frost told Sefcovic that France’s actions would be in breach of the trade and cooperation agreement between the EU and the UK, and that resolution or compensation would be sought through the levers in that deal. The French ambassador to the UK, Catherine Colonna, was asked to explain the French position after being summoned by the Europe minister, Wendy Morton, on Friday.

The UK government has approved 16 out of 47 applications for French boats to operate in the UK’s coastal waters. A further 14 applications are being considered where evidence of activity in those waters was limited, but 17 applications had been withdrawn by French applicants because of “poor evidence”.

Of greater concern to the French authorities is that 55 boats applying to fish in the waters off Jersey have been turned down by the island’s government due to lack of evidence that they have fished there for 10 days in any of the last three years.

Earlier in the day, the UK’s environment secretary, George Eustice, suggested that Emmanuel Macron’s hopes of being re-elected president may have been driving the diplomatic row.

Macron, who has been France’s president since 2017, is facing a difficult election in April, and votes in coastal communities may prove pivotal in the coming presidential campaign. “I don’t know, but there obviously is an election coming up in France, it may be that is a factor in this,” Eustice told BBC Radio 4’s Today programme.

Ireland’s EU affairs minister, Thomas Byrne, tweeted in solidarity with Paris: “The partnership between France and Ireland throughout Brexit has been strong. The trade and cooperation agreement is clear: vessels fishing in traditional waters should be allowed to continue. We support all efforts to resolve this quickly, to ensure trade and cooperation agreement compliance, and to protect impacted communities.”

Eustice, a longtime backer of Brexit, had also said France could expect retaliation if it followed through on its threats. “Two can play at that game,” he said. “It’s always open to us to increase the enforcement we do on French vessels, to board more of them, if that’s what they’re doing to our vessels – there are other administrative things we can require of vessels.”

The UK scallop vessel Cornelis Gert Jan was ordered to divert to the port of Le Havre on Wednesday after the French authorities said it was fishing in French waters without a licence. On Friday, Cyrille Fournier, the deputy prosecutor of Le Havre, where the boat was seized, said its captain had been asked to appear in court on 11 August 2022 on criminal charges.

The owner of the Cornelis has said the vessel had been fishing legally in French waters, but slipped off a list due to a clerical error.

Meanwhile, Frost also informed Sefcovic that a proposed 80% cut in the number of health checks on food and plants entering Northern Ireland from Great Britain, and a 50% reduction in the level of customs paperwork, “do not free up goods movements between Great Britain and Northern Ireland to the extent necessary for a durable solution”.

The government is currently considering triggering an article in the withdrawal agreement that will suspend the current post-Brexit arrangements for Northern Ireland.