Jeff Smisek, chief executive and chairman of the board of United Airlines, quit suddenly yesterday amid a corruption probe.
Two other executives of the third largest airline in the US also resigned.
Federal authorities are reported to be investigating whether Smisek sanctioned a money-losing flight to benefit the head of the Port Authority of New York and New Jersey.
United said that it was co-operating with investigators.
At the time the route operated from Newark, New Jersey, to Columbia, South Carolina, United Airlines was lobbying for improvements at Newark Liberty international airport, which the Port Authority owns, according to US media reports.
Former Port Authority chairman David Samson owned a weekend home in Columbia at the time.
United launched the twice weekly, direct flight shortly after Samson was appointed and cancelled it after he left the Port Authority.
Oscar Munoz, the chief operating officer CSX Corp, was named Smisek’s replacement as CEO of United.
United, confirming that Smisek had stepped down, said: “The company also announced that its executive vice president of communications and government affairs and its senior vice president of corporate and government affairs have stepped down.
“The departures are in connection with the company’s previously disclosed internal investigation related to the federal investigation associated with the Port Authority of New York and New Jersey.
“The investigations are ongoing and the company continues to co-operate with the government.
“The company’s internal investigation and the related circumstances do not raise any accounting or financial reporting concerns.”
According to the filing, United said that Smisek will receive a payment of $4.9 million as severance, in addition to a portion of his performance bonuses received in 2013, 2014 and 2015, which are still outstanding.
He will also remain eligible for his bonus this year. In exchange, he is subject to a non-disparagement clause and a two-year-long non-competition agreement in his termination deal.
He will also “hold in strict confidence any confidential information related to the companies”.