The Van Dijck left the port of Caen-Ouistreham on the Normandy coast, the port authority said, with its captain due to appear in court on May 15 to face charges.
The boat was impounded on Wednesday following an on-board inspection earlier this week on the edge of France's territorial waters, 12 nautical miles (about 22 kilometres) offshore.
French authorities ordered the captain to dump all 21 tonnes of scallops on board, a catch worth hundreds of thousands of euros (dollars) in the retail
market. Officials had earlier given a figure of 17 tonnes but that had not included the day's catch.
The incident followed clashes in October when the crews on five British trawlers claimed to have been surrounded and stoned by a flotilla of 40 French
boats while attempting to gather scallops from beds off the port of Le Havre.
The British fishermen, who called on the government to send the Royal Navy to protect them, claimed they had been fishing legally in international waters.
Their French counterparts accuse them of regularly encroaching into their territorial waters and undermining efforts to preserve stocks.
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The Van Dijck was the third British boat to have been detained and accused of illegal fishing in French waters in five months, following two similar interceptions in September.
A judgement on whether the first boat to be detained did actually breach the rules is due on January 16.