JetBlue planes sit at Ronald Reagan Washington National Airport in Arlington, Virginia, on January 18, 2022. (Photo credit: Stefani Reynolds/AFP/Getty Images via CNN Newsource)

(CNN) -- The US Department of Transportation has penalized JetBlue Airways $2 million over delayed flights, the first time the department has penalized an airline for delays.

According to the DOT, $1 million of the fine will go to JetBlue customers affected by delays or disruptions within the next year. The other half will go directly to the U.S. Treasury, with $500,000 due within 60 days and the other half due within one year after the first payment. The department also said it has investigations into other airlines for “unrealistic flight schedules,” which do not reflect actual flight departure and arrival times.

“The department will enforce the law against airlines with chronic delays or other unrealistic scheduling practices in order to protect healthy competition in commercial aviation and ensure passengers are treated fairly,” Transportation Secretary Pete Buttigieg said in a statement.

Under DOT rules, a flight is chronically delayed if it has been flown at least 10 times a month and arrives more than 30 minutes late more than 50% of the time. Cancellations are also included as delays in the DOT’s calculation.

The DOT found JetBlue to have operated four chronically delayed flights at least 145 times between June 2022 through Nov. 2023, with each flight delayed for five months in a row or more. The department warned JetBlue specifically about chronic delays on its flight between John F. Kennedy International Airport and Raleigh-Durham, and the airline continued to operate three more chronically delayed flights between Fort Lauderdale and Orlando, Fla. and JFK, and between Fort Lauderdale, Fla. and Windsor Locks, Conn.

A JetBlue spokesperson said in a statement that the airline appreciates how important it is for passengers to arrive at their destinations on-time, and that it works hard to operate its flights as scheduled. During the last two years, the airline said it had invested “tens of millions of dollars” to reduce delays, especially ones related to air traffic control shortages and challenges in the Northeast and Florida.

“While we’ve reached a settlement to resolve this matter regarding four flights in 2022 and 2023, we believe accountability for reliable air travel equally lies with the U.S. government, which operates our nation’s air traffic control system,” the statement read. “We believe the U.S. should have the safest, most efficient, and advanced air traffic control system in the world, and we urge the incoming administration to prioritize modernizing outdated ATC technology and addressing chronic air traffic controller staffing shortages to reduce ATC delays that affect millions of air travelers each year.”

In the latest DOT air travel consumer report for January to September of last year, 71.29% of JetBlue’s flights were on time, ranking nine out of 10 major U.S. air carriers. Hawaiian Airlines, for the same time period, flew 82.69% of its flights on time, ranking first among the reported airlines.

The DOT has beefed up passenger protections in recent years, including new rules requiring airlines to disclose fees on airfares and rules that require airlines to provide automatic cash refunds to passengers when owed. President-elect Donald Trump has nominated Sean Duffy, a former congressman and Fox Business host, to lead the department in his next term.

Future compensation will be valued at a minimum of $75 for each harmed passenger, the DOT said.

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