"We have worked a lot but we did not get enough. We are disappointed given farmers' involvement," Christiane Lambert, head of the FNSEA union, which organised the protests, said after meeting with Agriculture Minister Stéphane Travert.
Oil and gas major Total said on Tuesday that 3.5 percent of its petrol stations in France had run out of fuel after two days of blockade disrupted distribution.
The protests were triggered by France's decision to allow Total to use imported palm oil at a biofuel plant, which would compete with biodiesel made from locally produced oilseed crops, further souring relations between the EU's biggest farm sector and the government of President Emmanuel Macron.
The blockade concerns a total of 18 refineries and depots across France. Total, which operates 2,200 petrol stations, said all nine of its depots and all but one of its five refineries were blocked.
"There are some difficulties in supplying petrol stations particularly in Paris and the Ile-de-France region," a Total spokesman said Tuesday.
Total has urged customers not to rush to petrol stations to fill their tanks, which could spark panic buying and shortages.
French authorities last month gave Total permission to use palm oil as a feedstock at its La Mede biofuel refinery in southern France, infuriating farmers who grow crops such as rapeseed. Environmentalists also blame palm oil cultivation for deforestation in Southeast Asia.
Total argues its plans call for using less palm oil than allowed by the authorities, offer an outlet for 50,000 tonnes of locally produced rapeseed, and will develop large-scale recycling of used oil and fat.
But Lambert, the FNSEA union leader, said 50,000 tonnes was "not enough" and that the price needed to be based on producers' costs, not on palm oil prices.