Canada's competition watchdog is accusing Montreal-based travel company FlightHub of garnering millions of dollars in revenue from hidden fees.

The Competition Bureau has signed an agreement that commits the online travel agency to avoid giving a "false or misleading general impression" to the public regarding airfares, seat selection and flight rebooking or cancellation.

None of the allegations have been proven and FlightHub says it is co-operating with the ongoing investigation.

Earlier this year the watchdog executed search warrants and seized records at FlightHub's headquarters.

The bureau says it has reviewed thousands of consumer complaints about online marketing by FlightHub and its sister travel agency JustFly.

Montreal-based online travel agency FlightHub's headquarters was searched by Canada's Competition Bureau earlier this year. (FlightHub)

The agreement is slated to remain in effect until the bureau's investigation is resolved by a deal with FlightHub or a decision by the quasi-judicial Competition Tribunal.

FlightHub said it has introduced changes to its platforms to address the bureau's concerns and voluntarily entered into a temporary consent agreement "in the spirit of collaboration."

"Our goal is to offer our customers complete transparency when it comes to the flights they are booking, the fees they are being charged and the airlines' policies," said Christopher Cave, FlightHub's chief operations officer, in an email.

Last month, the state of California filed a lawsuit against FlightHub and JustFly over alleged "deceptive" business practices that include "false" and "hidden fees."