The minister called on angry protesters to join talks to find "adequate solutions". "We're going to ask our members to suspend with immediate effect their blockade of the different sites", Jeremy Decerle, leader of the FNSEA's youth-wing, told reporters.
Farmers in France have blocked access to several oil depots and refineries in protest - that is organized to last three days - against the proposed use of imported palm oil at a Total biofuel plant.
Total's 253,000 barrels-per-day (bpd) Gonfreville refinery and nearby oil depot, its 109,000 bpd Feyzin refinery, the 220,000 barrels-per-day (bpd) Donges refinery and 102,000 bpd Grandpuits refinery were among those blocked by farmers.
Christiane Lambert, President of France's farmer's union group FNSEA, walks past tractors during a protest by French farmers to block the French oil giant Total refinery in Donges, France, June 11, 2018.
It urged clients not to rush to petrol stations to fill their tanks, which could spark panic buying and shortages.
Organisers say the farmers' blockades are aimed at pressuring the government into curbing palm oil use at La Mede and to address other grievances such as imports of South American meat.
Agriculture Minister, Stephane Travert, said today that the occupation of refineries and deposits is illegal, and ruled out that this will cause a shortage of fuel in the country.
"Our target is the state", Lambert said, adding that Total's decision on palm oil was "the last straw".
Total committed to use less than 300,000 tonnes of crude palm oil per year at its La Mede biofuel refinery out of a total processing capacity of 650,000 tonnes, and to use 50,000 tonnes of locally grown rapeseed.
Besides a ban on palm oil imports, she wants the government to outlaw agriculture imports produced using fertilisers, herbicides and other products prohibited in the European Union as part of an agriculture law that will be debated in the Senate starting June 26.
Indonesia and Malaysia are the two largest producers of palm oil.