Shares of Southwest Airlines (LUV) fell Thursday after the Department of Transportation sued the airline over a pair of "chronically delayed flights."

The federal agency said late Wednesday that Southwest operated two flights—from Chicago to Oakland and Baltimore to Cleveland—that qualified as "chronically delayed" for five straight months in 2022.

A flight is defined as "chronically delayed" when it is operated at least 10 times a month and arrives at least 30 minutes late for more than half the time, the agency said in its court filing Wednesday. The DOT considers taking action once a chronically delayed flight is advertised at its normal time for more than four months in a row, as "unrealistic scheduling" can give airlines a competitive advantage.

"Southwest is disappointed that DOT chose to file a lawsuit over two flights that occurred more than two years ago," a Southwest spokesperson told Investopedia. "Since DOT issued its Chronically Delayed Flight (CDF) policy in 2009, Southwest has operated more than 20 million flights with no other CDF violations. Any claim that these two flights represent an unrealistic schedule is simply not credible when compared with our performance over the past 15 years."

The DOT also fined Frontier Airlines (ULCC) $650,000 on Wednesday for operating "three chronically delayed flights between August 2022 and April 2023," and fined JetBlue Airways (JBLU) $2 million earlier this month for operating "four chronically delayed flights at least 145 times between June 2022 through November 2023."

Citi Downgrades Southwest

Separately, analysts from Citi on Wednesday downgraded Southwest's stock to "sell" from "neutral" and cut their price target by $2 to $29.50, citing concerns that Southwest stock trades at a higher premium than some of its U.S. airline rivals. They said they expect a "correcting" in Southwest's valuation in coming months.

Southwest shares recently were down more than 3%. They are up more than 10% over the past 12 months.