After several hours of stand-off, the protest turned violent. A car was overturned, bins were set on fire and windows were smashed by flares.
Riot police lined up behind a barbed-wire barricade in front of the European Commission responded by attempting to disperse the crowd with water cannons and baton charges.
Earlier, a delegation of fishermen met senior EU officials briefly outside the Commission's headquarters to explain their grievances and demand emergency aid from both the EU and their countries' governments.
Philippe Margoud, a fisherman from the French Mediterranean port of Agde, said the price of marine diesel had gone up by a third in the past four months.
EU FUEL TAX RULES
EU rules state the VAT on fuel cannot be less than 15%
Member states are free to set VAT rates at or above that minimum
Changing VAT minimum requires proposal from European Commission and unanimous agreement of all member states
Also minimum EU-wide excise duty of 330 euros (£260) per 1,000 litres (220 gallons) of diesel
"Fuel is too expensive. France put a mechanism in place two years ago which provided the fishermen with a compensation package, and Europe said no," he said.
"That's why we came here, to tell Europe to stop getting in the way of the French government trying to help us."
However, the EU officials stressed that any fuel subsidies would be illegal under European law and unsustainable in the long term.
EU rules state that the value-added tax (VAT) rate on fuel cannot be less than 15%. Member states are free to set VAT rates at or above that minimum.
"There is a problem of high costs at the time when the sector is also in a situation where there is overcapacity and where there is a need for restructuring," said Patrick Tabone, the chief political adviser of the EU fisheries commissioner.
"What we need to ensure is that the responses we come up with are a real help to the sector, not only in the short term, but in the long term."
The BBC's Dominic Hughes in Brussels says that this is not a message the angry fishermen will want to hear.
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