Ryanair did not respond to requests for comment.
The 149 passengers were heading to London were already on board and had to disembark when the aircraft was seized on Thursday evening, the airport said.
The dispute was caused by French subsidies paid to Ryanair for flights from Angoulême regional airport between 2008 and 2009, which the European Commission later deemed illegal.
Following the commission's 2014 ruling that the payments gave Ryanair an unfair advantage, around half the subsidies were repaid.
The French civil aviation authority seized the aircraft on Thursday at Bordeaux airport ahead of its planned flight to London Stansted, the latest episode in a string of troubles for the low-priced Irish carrier.
The French civil aviation authority did not say how much money was involved, but regional airport officials said the sum was €525,000 (£457,000).
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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.
In France, 149 passengers were preparing to take off for London late Thursday when French authorities ordered their Ryanair Boeing 737 impounded. "By this act, the State reaffirms its desire to guarantee the conditions for fair competition between airlines and between airports".
"Just because we manage a little airport in Charente it doesn't mean we are not going to defend ourselves", he added.
And last week ministers from five European governments warned Ryanair that it could face legal trouble if it ignores national labour laws after a series of strikes across the continent.
But despite flight cancellations, Ryanair reported an 11% rise in traffic in October, as it carried 13.1 million passengers.
Profits fell seven per cent to £1.06 billion (€1.2 billion) in the six months to September 30.