The Transportation Department announced on Friday a $2 million penalty against JetBlue Airways for operating several flights on the East Coast that chronically arrived late in 2022 and 2023. Half of the money collected will go to the impacted passengers.

The penalty is the first time that the D.O.T. has fined an airline for chronic delays, which the federal agency defines as flights that are flown at least 10 times a month that arrive more than a half-hour late more than 50 percent of the time.

“Illegal chronic flight delays make flying unreliable for travelers. Today’s action puts the entire airline industry on notice that we expect their flight schedules to reflect reality,” Transportation Secretary Pete Buttigieg said in a statement.

The D.O.T. said it had warned JetBlue about persistent delays on its flights between Kennedy International Airport and Raleigh-Durham International Airport in North Carolina. It added that carriers have a “legal responsibility to avoid chronic delays” and that these flights for months was unfair and deceptive.

The four routes under scrutiny flew between J.F.K. and Raleigh-Durham Airport; J.F.K. and Fort Lauderdale-Hollywood International Airport in Florida; J.F.K. and Orlando International Airport; and Fort Lauderdale-Hollywood Airport and Bradley International Airport in Connecticut. Between June 2022 and November 2023, the flights were chronically delayed five months in a row. More than 70 percent of the disruptions for these flights were caused by the airline, according to estimates from the Bureau of Transportation Statistics.

“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,” Mr. Buttigieg said.

Derek Dombrowski, a spokesman for JetBlue, said in a statement that the airline had invested tens of millions of dollars to reduce flight delays over the last two years and had seen “significant operational improvements.” Mr. Dombrowski also said that air traffic control issues had contributed to the airline’s operational challenges in the Northeast and Florida.

Last week, JetBlue made headlines when a flight from Turks and Caicos bound for Boston was delayed more than 24 hours, stranding passengers with no accommodations.

From January to September of last year, about 71 percent of JetBlue’s flights were on time, according to data from the Transportation Department, and the carrier was ranked second to last in on-time performance of the largest 10 domestic airlines (Frontier Airlines was in last place). During this same time period, more than 9 percent of JetBlue’s flights were delays caused by the airline, according to the Bureau of Transportation Statistics.