The aviation authority called it "regrettable that the state was forced" to evacuate the plane yesterday.
The European Commission later ruled those funds illegal, saying they gave Ryanair an unfair economic advantage.
French authorities said on Friday they seized a Ryanair plane, forcing 149 London-bound passengers off the aircraft, to get the Irish low-priced airline to repay illegal public aid, the latest in a string of troubles for the carrier.
Villat added he expected Ryanair to pay the remaining sum by the end of Friday. Some 149 passengers on board had to wait five hours before being able to take off from the Bordeaux-Merignac airport in another Ryanair aircraft.
Ryanair owed €525,000 to the department that it had received in aid when the company operated an Angoulême-London route.
It was not immediately clear how much money French authorities were trying to reclaim from Ryanair.
"By this action, the government reaffirms its intention to guarantee the conditions of fair competition between airlines and between airports".
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In reality, Ryanair's plane was seized because of overdue bills. Ryanair's fleet is made up mainly of Boeing 737-800 aircraft, which have a list price of more than $90 million each.
"We will investigate whether regional and local authorities in Germany, against the rules, gave an unfair advantage to Ryanair over its competitors", European Union competition commissioner Margrethe Vestager said.
HuffPost UK has contacted Ryanair for comment.
It is the latest in a series of setbacks for Ryanair, which has recently faced a series of strikes by pilots and cabin crew across Europe.
Profits fell seven per cent to £1.06 billion (€1.2 billion) in the six months to September 30.
Ryanair is also fighting an order by Italian regulators to suspend a charge for carry-on bags.