The vouchers were given to passengers who voluntarily gave up seats when a flight was overbooked, the Department of Transportation said.
Travelers found after they had accepted the vouchers that a $30 fee was imposed if they tried to redeem them. Passengers were also not told the vouchers could not be redeemed on American Airlines' Web site, the department said.
"American stopped requiring fees for tickets purchased by phone using vouchers about four years ago but continued to require fees for tickets acquired at airport counters until late last year, and even today passengers cannot use bumping vouchers to purchase tickets online," the department said in a statement.
"When passengers volunteer to give up their seat on an oversold flight, they are entitled to be fully compensated -- not to find out later that they're getting $30 less," said U.S. Transportation Secretary Ray LaHood.
"Passengers deserve to be treated fairly when they fly, and especially when they've volunteered to give up their seat because the airline overbooked their flight."
The department said it was the first fine imposed on an airline for inappropriate handling of overbooked flight travel vouchers.