Flight comparison websites could be forced to disclose the commission they receive from airlines as part of a wider probe.
Regulators are investigating the entire online price comparison industry.
Sites such as Skyscanner, Cheapflights and TravelSupermarket are to be scrutinised by the Competition and Markets Authority, which said that it would stamp out any anti-competitive practices it found.
Comparison websites and mobile phone apps are considered advantageous for consumers but the CMA is concerned that some may not be trustworthy and may be striking deals with suppliers that restrict competition, The Times reported.
Previous investigations have involved energy switching services and websites selling motor insurance and other financial services but this is understood to be the first with flights as a particular line of inquiry.
The CMA said that it would also focus on broadband, home insurance and credit cards.
It said that it wanted to look at flights sites as they were a large expenditure item for families and had an important influence on customer behaviour.
The CMA will look at whether consumers would benefit from being made aware of how comparison sites earn money and the impact this might have on the services they offer.
It will also consider whether the arrangements they have with the suppliers that sell through them might restrict competition.
CMA acting chief executive, Andrea Coscelli, said: “Some people have raised concerns about certain issues, including whether consumers can trust the information that’s available.”
The inquiry will take a year and if problems are found, the CMA can seek a more in-depth investigation.
MoneySuperMarket, which owns Travelsupermarket, said that it looked forward to co-operating.
“We have helped 3.5 million households save £900 million in the first half of this year,” it said.
Skyscanner said it hoped that the CMA would highlight players that placed the needs of consumers at the heart of their business.