EU transport ministers approved plans on Thursday night to offer passengers up to £375 ($590) in compensation for delayed or cancelled flights.
But budget airlines such as Ryanair, Easyjet and Buzz opposed the plans, suggesting the compensation should be linked to the cost of the flight.
And they have now warned that the increased charges could mean higher fares for passengers.
Price hike?
Airlines often sell more tickets than there are seats on particular flights, working on the principle that a certain number won't turn up.
"
It is ludicrous not to have the level set in relation to airfare price
"
Paul Fitzsimmons
Ryanair
When too many passengers check in, some are moved to a later flight in a practice known as "bumping".
EU transport ministers have now approved plans to pay about £125 to passengers on short-haul flights and up to £375 for longer flights.
The sharp rises could mean an end to the 'bucket shop' flights which British passengers have been enjoying.
Less profit
Ryanair's chief executive Michael O'Leary told the BBC that the proposals were unfair and would mean a rise in airfares.
The airline's communications chief Paul Fitzsimmons said: "It is ludicrous not to have the level set in relation to airfare price. It has to be in relation to what the passenger has paid."
Last month, when the law passed its first reading, rival budget airline Easyjet warned that the new rules could spell the end of some airlines.
David Nichols, a director of Easyjet, said: "In a couple of areas this will certainly cost more and airlines will either have to accept less profit or put up ticket prices.
"Some airlines could go to the wall over this."