The passengers had gone through passport control and security and were about to walk on the tarmac to board the plane when airport authorities told them to turn around, passenger Boris Hejblum said.
The airline today paid...
The European Commission later ruled around £873,000 (€1million) in subsidies paid to Ryanair were illegal and ordered the Irish carrier to repay all the money.
Ryanair had been ordered to repay €1 million of subsidies, but the French government said it had only paid back half the money.
Passengers from the Thursday flight were put on another plane, which eventually took them to their destination at London's Stansted airport - five hours late.
The Local has approached Ryanair for comment.
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The French civil aviation authority said it had seized the plane at Bordeaux-Merignac airport as a "last resort" after France repeatedly tried to get Ryanair to pay back regional funds to the airline in 2008/09.
"By this action, the government reaffirms its intention to guarantee the conditions of fair competition between airlines and between airports".
Ryanair owed €525,000 to the department that it had received in aid when the company operated an Angoulême-London route.
French airport official Didier Villat told Sud Ouest newspaper: "To my knowledge it's the first time a Ryanair plane has been seized in this way".
In October, EU anti-trust authorities opened an investigation into whether Ryanair benefited from measures at a German airport that give the Irish low-priced carrier an unfair leg-up over competitors.
Ryanair has been hit by a number of setbacks in recent months, with pilots and cabin crews across Europe going on strike.
Ryanair is also fighting an order by Italian regulators to suspend a charge for carry-on bags.