Tempers flared on Monday in the Bay of the Seine off the coast of the French port of Le Havre.
The dispute drew in 40 French boats and five British trawlers, according to the Marine Management Organisation (MMO).
The British fishermen told the MMO that stones and flares were aimed at them when the French boats encircled their vessels as they attempted to force them away from the French-controlled waters.
Such confrontations are rare in the waters of the Channel.
Clinton Powell, a fisherman from Devon in southwest England, told the BBC: "Something has got to be done and we need naval protection."
Rod Henderson, head of Coastal Operations for the MMO, said: "As soon as the MMO was made aware of the situation, our officers contacted the French authorities and encouraged them to intervene.
"They did and are continuing to deal with this matter.
"The MMO is continuing high-level discussions with French counterparts to seek assurances that these issues will not recur."
French scallop fishermen complain that they are subject to quotas and their season is shorter than their British counterparts.