The government body said that it had been in discussion the owners of the two sites over the course of the year, “in relation to a number of issues concerning price transparency”.
It added the OTAs, which are both part of the eDreams Odigeo travel group, had “failed to address these concerns and they have now been notified that a CAA investigation is underway”.
Separately, the Advertising Standards Authority published a ruling upholding a complaint against Opodo relating to misleading advertising and pricing.
The ASA has also asked for this decision to be extended to cover the website of eDreams. The CAA welcomes both these decisions.
The CAA said it would “continue to monitor the practices of airline operators and major travel agents in relation to price transparency and trading fairly to ensure that consumers are not misled and have access to comparable information on prices”.
A spokesman for eDreams Odigeo said: ""eDreams ODIGEO aims to provide best-in-class websites which offer consumers the widest possible flight choice, at the lowest prices available.
"We take the CAA’s concerns very seriously and will continue to co-operate with them to address the findings of their investigation."