The Government is “urgently” investigating following reports that the trawler has been detained off the coast of France amid ongoing disputes about fishing rights.
Two boats were fined on Wednesday after one failed to comply with checks by police and the other was found not to hold a proper licence, according to the French maritime ministry.
French authorities said the UK’s failure to comply with trade agreements is “unacceptable” and they will defend the rights of their own fishermen.
It is understood the trawler being held is called the Cornelis Gert Jan, which operates in and out of the port of Shoreham, in Hampshire.
The boat is operated by MacDuff Shellfish of Scotland.
MacDuff Shellfish told the BBC its fishing activity was "entirely legal" and the vessel was "legally fishing for scallop" in French waters..
The firm said its boat was just "another pawn" in the ongoing France-UK fishing row and urged the UK government to "defend the rights of the UK fishing fleet".
A statement from the French maritime ministry said checks had been carried out on the boats in the Baie de Seine, near Le Havre, in the north of the country.
One trawler was fined for obstructing checks after it initially refused a request to be boarded by police, the statement said.
It was later found not to have been in breach of regulations.
The ministry said the second boat was not on a list of UK vessels with licences granted by the European Commission and France.
The boat was then ordered to divert to Le Havre.
Members of the fishing industry said the incident has been “politicised” by the French, who are “determined” to escalate the issue.
A UK Government spokesperson said: “France’s threats are disappointing and disproportionate, and not what we would expect from a close ally and partner.
“The measures being threatened do not appear to be compatible with the Trade and Co-operation Agreement (TCA) and wider international law, and, if carried through, will be met with an appropriate and calibrated response.
“We will be relaying our concerns to the EU Commission and French government.
“The UK stands by its commitments in the TCA and has granted 98% of licence applications from EU vessels to fish in our waters.
“All our decisions have been fully in line with this commitment.
“We also support Jersey and Guernsey’s handling of fisheries licensing decisions, which has been entirely in line with the provisions of the TCA.”
Deidre Brock, the SNP's environment spokesperson asked an Urgent Question on the matter in the House of Commons at 10:30.
She pressed George Eustice to offer more details on the Scottish vessel detained by the French authorities, adding: “We have a skipper of a Scottish scalloping vessel due in court, it’s simply not good enough that the Secretary of State doesn’t have answers to those questions.”
Mr Eustice, on the vessel thought to be detained, said: “What I’ve been able to establish so far in respect of that vessel is that they were on the list that was provided by the MMO (Marine Management Organisation) initially to the European Union.
“The European Union therefore did grant a licence. We are seeing some reports that for some reason they were subsequently withdrawn from the list, it’s unclear why that might have been at the moment.”
Mr Eustice said he was awaiting further details from Marine Scotland and is expecting a response in the “next hour or so”.
France’s threats to block British boats from French ports and tighten checks appear to breach international law, the Environment Secretary has suggested adding that the UK would deliver an “appropriate and calibrated response” should France follow through with the measures.
George Eustice added that he had spoken with Virginijus Sinkevicius, the European Commission’s maritime affairs and fisheries commissioner, about the comments made by French officials.
He said: “The UK stands by its commitments in the trade and co-operation agreement and, as I’ve said, has already granted 98% of licence applications from EU vessels to fish in our waters.
“All of our decisions have been fully in line with this commitment.”
Home Secretary Priti Patel has described the detention of a British fishing trawler by French authorities as “disappointing”.
When asked if she was concerned about the latest action in the dispute about fishing rights and whether she had spoken with her French counterpart, she said: “It is disappointing, and we as a country fulfilled all our obligations under the TCA.
“But at the same time, discussions across Government will continue, both at commission level but also with counterparts within the French administration.”
France is understood to be angry by a decision from the UK and Jersey last month to deny fishing licences to dozens of French boats, and argued that it breached the Brexit deal.