The US has hit Lufthansa with a record $4m (3m) penalty after the airline barred Jewish passengers from a 2022 flight because some allegedly refused to follow rules requiring face masks.

The Department of Transportation said Lufthansa discriminated against the passengers, treating them "as if they were all a single group", though many were not travelling together and did not know one another.

It said the penalty was the largest it had ever issued against an airline for civil rights violations.

Lufthansa said in the consent order that it was agreeing to the payment to avoid litigation but denied discrimination, blaming the incident on "an unfortunate series of inaccurate communications".

"Lufthansa is dedicated to being an ambassador of goodwill, tolerance, diversity, and acceptance," the company said in a statement, adding that it had cooperated with the investigation and remained focused on training for its staff.

The episode involved passengers who were travelling from New York to Budapest, with a connection in Frankfurt, in May 2022.

Many of the passengers were male, wearing "distinctive garb typically worn by Orthodox Jewish men" and had used the same handful of travel agencies to book their tickets, according to the DOT.

During the first flight, the captain alerted Lufthansa security that some passengers had failed to follow crew instructions requiring masks, and barring gathering in aisles and other places on board.

The alert led to holds on tickets of more than 100 passengers, all of them Jewish, which led to them being blocked from their connecting flight.

The DOT said Lufthansa recognised that the action also would hurt people who had complied with the instructions but "concluded it was not practical to address each passenger individually".

The majority were rebooked on other flights the same day.

“No one should face discrimination when they travel, and today’s action sends a clear message to the airline industry that we are prepared to investigate and take action whenever passengers’ civil rights are violated,” US Transportation Secretary Pete Buttigieg said.

The DOT said passengers interviewed for the investigation said they had not witnessed misbehaviour and Lufthansa later failed to identify any one passenger who had not followed the rules.

But in the consent order, Lufthansa said its staff was unable to single out passengers because "the infractions were so numerous, the misconduct continued for substantial portions of the flight and at different intervals and the passengers changed seats during the flight".

The DOT said it was requiring Lufthansa to pay $2m and would give the airline credit for $2m it has already paid to passengers as part of a legal settlement.