"For the past two days, since there have been operational problems at the refineries and blockades of depots, we have ... been using reserve supplies," Francis Duseux told French radio.
The move marked the first time since 2010 that France has had to dip into its strategic oil reserves.
"At the worst, if the situation remains very tense, we will do this for three months," Duseux said, adding that consumers had "contributed a little" to the problem because they were panic-buying.
"We are all filling our tanks as a precaution because we are afraid, and consumption has multiplied by three times or even five times in some areas," he said.
French President François Hollande sought to calm fears, saying on Wednesday that "everything will be done to ensure the supply [of petrol] for the French people and the economy".
The blockades are the latest battle in the war over a labour reform that the government says is crucial to fight rampant unemployment – stuck at more than 10 percent of the workforce – and which aim to make hiring and firing easier. The powerful CGT union says the reforms will unravel protective labour regulations, even though other unions back it.
Ministers went on radio morning shows Wednesday to say the government would stand firm, while CGT chief Philippe Martinez told RTL radio that his union would press on with its strikes.
So far the industrial actions have affected oil depots and refineries as well as train and metro strikes. On Wednesday three out of four high-speed TGV trains were running and only four of five regional RER trains were operational.
Police used water cannons in the early hours of Wednesday to dislodge some 80 unionists who were blocking a fuel depot at Douchy-les-Mines in northern France, union and police officials said. Other depots were unblocked by police on Tuesday.
Undeterred, CGT chief Martinez told France Inter: “We will carry on.”
CGT workers have voted for a 24-hour strike starting at 7pm GMT on Wednesday at the Nogent-sur-Seine nuclear plant southeast of Paris and workers at other nuclear plants will meet today to decide on possible further strikes, said Laurent Langlard, a spokesman for the CGT’s energy federation.
(FRANCE 24 with AFP, REUTERS)