Passengers using a low-fare airline will now have to pay for their luggage to be put in the hold of the aircraft.
Passengers pre-booking luggage will be charged a lower rate
Flybe said it will charge £4 for each piece of hold luggage or £2 if people have pre-booked hold bags in advance.
At the same time the airline, whose departure airports include Birmingham, Exeter, Norwich and Southampton, is knocking £1 off its fares.
The Air Transport Users Council (AUC) said as long as fares were reduced then most passengers would not be concerned.
James Fremantle, industrial affairs adviser at the AUC, told the BBC News website: "The change will benefit some passengers but not others.
"It will be easier for customers to accept if tickets are cheaper but we'll just have to wait and see if they do drop prices or not.
"What we would be worried about is that people were made aware of the charges before they book."
He said he expected other low-fare airlines to follow Flybe's example.
Flybe said it would double the weight allowance for hand luggage on flights from 11lb (5kg) to 22lb (10kg) and the hold baggage allowance to 55lb (25kg).
Jim French, Flybe chairman and chief executive, said: "For the first time passengers checking bags on to flights will pay for the service they use rather than the cost being unfairly spread across all people on the aircraft."