Around 35 boats had left various ports in Normandy early on Tuesday morning to confront around five British boats that were fishing for scallops in global waters in the English Channel.
It comes just a day after news emerged French President Emmanuel Macron rejected PM Theresa May's Chequers blueprint, which would see the United Kingdom abiding by European Union rules in return for free trade - effectively slashing her hopes of hammering out a deal with the European Union by the October deadline.
"This kind of event is extremely risky at sea", she said, adding that authorities would remain vigilant for signs of flare-ups.
A video published by French media shows a Scottish scallop dredger, the Honeybourne 3, colliding with French vessels.
French fishermen accuse the British of depleting scallop stocks in what they consider their home waters.
One of the British ships, The Golden Promise, had a window smashed by an airborne can, while another suffered fire damage after a flare was thrown at it, Mr Portus said.
The maritime prefecture, which sent a boat to the scene, reported "altercations between French fishermen and British fishermen" but no injuries.
British crews have now accused the French of destroying and damaging crab pots off the coast of Newquay and Padstow as they trawl the waters off Cornwall.
"The scallop fishery is regulated at the national level and over the past years common management measures have been agreed between France, the United Kingdom and Ireland", he said.
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"Scallops are plentiful and they're expensive", he said.
An EU spokesman, Daniel Rosario, called for a negotiated solution.
They catch just 6% of the scallops in the area, he said, so "if there's any accusation of over fishing it's not on the United Kingdom fishermen, it's on the French fishermen". "We're doing nothing wrong and what we can't do is be bullied".
"So it is in the interest first and foremost of the fishermen that this agreement is in place".
But she questioned whether French authorities were "turning a blind eye" while their fishermen "took the law into their own hands".
But British ships can still fish for the prized delicacies in worldwide waters off the French coast.
"The French went to contact the British to stop them working and they clashed with each other".
The clash comes following the breakdown of a deal between the warring fisherman.
Mr Rogoff said the French trawlermen wanted the visiting fleet to stay north of a line running from Barfleur in Normandy to Cap d'Antifer to the east to avoid running supplies down.
The clashes happened in the scallop-rich waters of the Baie de Seine area of Normandy, 12 nautical miles out to sea, where the Brits are legally entitled to fish.