WASHINGTON — The Department of Transportation said Friday that it has fined United Airlines $1.9 million for keeping thousands of passengers stuck on planes for hours in violation of federal rules, the largest penalty of its kind.

The department pointed to 20 domestic flights in which passengers were held on the tarmac for longer than three hours, and five international flights where the delay was at least four hours. In all, 3,218 passengers were affected. Almost all the incidents involved bad weather, according to an order spelling out the basis for the fine.

United spokesman Charles Hobart said the airline has been making improvements to its operations since 2015 to avoid lengthy delays, developing a system to identify airports that are accessible during bad weather, and investing in equipment so airports can handle a variety of aircraft.

“The safety of our customers and employees is always our first priority — particularly during severe weather,” Hobart said. “We remain committed to fully meeting all DOT rules and will continue identifying and implementing improvements in how we manage difficult operating conditions while maintaining the safety of our customers and employees.”

The fine was a result of a settlement between the government and the airline, but the order says United disputed some of the facts. Hobart said that some of the 25 incidents stretched back five years and that United and its partners had operated 8 million flights in that time.

“United believes that both it and the Department ultimately want what is best for passengers — to safely move passengers to their destinations and around adverse weather as quickly as possible,” according to the order. “But, with regard to some of the flights in this order, United respectfully disagrees with the Department that enforcement action is warranted.”

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Five of the flights the Transportation Department identified occurred on a single day in 2019, when a snowstorm at Chicago’s O’Hare International Airport led United to divert planes to Dane County Regional Airport in Madison, Wisconsin. Because of the number of diverted flights, the Transportation Department said, “United’s resources at the airport became overwhelmed.”

In one case, passengers sat on a plane for four hours and one minute.

Of the $1.9 million, United is required to use $750,000 to compensate passengers on the affected flights and others who have faced delays. The airline will get to keep $200,000 to cover the cost of developing a diversion management system.

The Transportation Department closely regulates delays, which can occur either before planes take off or after they land. Airlines are required to let domestic passengers off within three hours and international passengers within four hours. After two hours, airlines are required to offer stuck passengers water and a snack.

United was previously fined $750,000 in 2016 for breaking the rule, and other major airlines have also faced hefty penalties.

The new fine comes as the Biden administration promises to strengthen legal protections for airline passengers and tackle anti-competitive practices in the industry. The Transportation Department is considering a rule on refunds for fees when bags are delayed or Wi-Fi doesn’t work. On Tuesday, the Justice Department sued to block an alliance between American Airlines and JetBlue Airways that it said would drive up ticket prices.