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Do airlines give the whole story on flight delays?

Are airlines providing their passengers all the available information when it comes to potential flight delays?

The CEO of flight-tracking service FlightAware told CNBC: Maybe not.

"The airlines provide the information they want to give you," Daniel Baker, the company's CEO, claimed in a "Squawk Box" interview Wednesday. "They want to be able to control" whether to deem a flight delayed or canceled.

(Weather.com: Latest forecast and Thanksgiving travel updates)

Responding to those assertions, JetBlue COO Rob Maruster said in a separate "Squawk Box" appearance, "We won't post delays for more than 90 minutes, because we don't want to lose all the customers."

"It's not that we're not trying to be transparent," he continued. "If that delay gets pulled in, we want the customers there" at the airport so they don't miss their flight.

"The worst thing you can have on a day like today is somebody saying, 'Well, you said it was a three-hour delay and then you left [only] an hour late. I'm here. I missed the flight. Now how am I going to get home for Thanksgiving?'"

For its part, United said its goal is to provide "customers with the most up-to-date information about their flight status so they can make informed decisions in the case of delays or cancellations."

US Airways said it "uses all sources of information" and strives for transparency to provide "customers with accurate, timely information concerning flights that may be delayed or even canceled."

Travelers check in for holiday flights at Chicago's O'Hare International Airport on Wednesday.
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Travelers check in for holiday flights at Chicago's O'Hare International Airport on Wednesday.

On Wednesday, AAA said more than 43 million Americans are expected to be on the move, as a pre-Thanksgiving storm in the southern and eastern portions of the country made travel difficult. Three million of those people will travel by air, but may find that delays were not as bad as had been expected early Wednesday, at airports from Washington to Philadelphia, to New York.

Flight delays can cost airlines about $78 a minute, according to the trade group Airlines for America. So it's no wonder carriers want to minimize possible delays.

(Read more: Chart of the Day: Airlines losing $78/minute today?)

In addition to providing consumers flight information, FlightAware's Baker said, "We provide a lot of operational tools to the airlines and to aircraft operators ... to help them know where their planes are, when to expect delays and help with routing."

JetBlue's Maruster said he thinks FlightAware is a "great product ... [but] what they're not good about knowing is what flights are at risk of being canceled—if there's going to be a large cancellation event." He stressed, "That's where it really becomes airline dependent."

Baker readily admitted that the airlines are the authoritative source on flight cancellations, but FlightAware tries to "figure before anyone if a flight is going to be delayed."

FlightAware aggregates hundreds of different data sources in real time, he explained. "We're less reliant on when the airline says that your flight is going to depart. And we're more reliant on where is that plane right now."

Whether flights are delayed or not, no airline wants to send a passenger to another carrier, JetBlue's Maruster said. "This is why you saw coming into today there are a lot of fee waivers for all airlines."

By CNBC's Matthew J. Belvedere. Follow him on Twitter @Matt_SquawkCNBC.

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