A union representative claims police took part in "unprecedented violence"
Water cannon and tear gas were used by French police to break up a picket at the Fos-sur-Mer refinery in Marseille, according to a trade union.
The General Confederation of Labour (CGT) said workers striking outside were blocking access and not allowing trucks or vessels to load or unload.
Union representative Emmanuel Lepine said about 40 busloads of riot police took part in an early morning operation "of unprecedented violence".
The clashes followed warnings from the government that attempts to disrupt fuel supplies would not be tolerated.
The standoff marked an escalation in the dispute over planned labour reforms, which would make it easier for employers to hire and fire workers.
In protest, the hardline CGT union is trying to put into action full-scale rolling strikes at a number of ports, oil refineries and railways.
The union says all eight refineries in the country are now closed because of the industrial action and that output is going to fall by at least half.
Workers at the Fos refinery are also taking part in a number of other pickets blocking deliveries in and out of fuel distribution depots.
French Prime Minister Manuel Valls has said further pickets will be cleared and insists there are sufficient fuel supplies.
Despite this, many petrol stations have partly or completely run dry.
The French government pushed through a new Labour reform bill earlier this month without having a vote in parliament, which sparked a number of street protests.
CGT has also called for strikes on the national railways and on the Paris subway to be held a week before the Euro 2016 soccer tournament opens.