It was "regrettable" that the plane had to be impounded "as a last resort" after several efforts to get Ryanair to repay the subsidies had failed, the directorate said.
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.
'By this action, the government reaffirms its intention to guarantee the conditions of fair competition between airlines and between airports, ' it said.
The authority did not specify the amount owed by Ryanair.
Didier Villat, president of Syndicat Mixte Des Aeroports De Charente (Charente airport union), said Ryanair had reimbursed half the figure given to the Irish company by regional authorities but that €525,000 remained.
"Just because we manage a little airport in Charente it doesn't mean we are not going to defend ourselves".
French aviation agency spokesman Eric Heraud said regional authorities who originally gave the subsidies had been trying since 2014 to recover the money, and sent its final legal warning in May.
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.
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.
The Local has approached Ryanair for comment. Besides charging for seating choice and food - now standard practice on budget flights the world over - it also has travelers pay for any carry-on bag that's larger than a purse.