The chief executive and two senior officials of United Airlines resigned on Tuesday amid a federal investigation into whether the airline had traded favors with the chairman of the Port Authority of New York and New Jersey.

The United States attorney for New Jersey has been investigating whether United, the nation’s third-largest airline, agreed to reinstate money-losing flights to the airport nearest the weekend home of the authority’s chairman, David Samson, in return for improvements the airline wanted at Newark Liberty International Airport, where it is the biggest carrier.

The resigning chief executive, Jeff Smisek, is the former chief executive of Continental Airlines and prevailed in his bid to lead United after the two airlines merged in 2010. But United’s performance since the merger has lagged rivals’ and angered passengers, as it suffered from delays, a breakdown of its reservation system and other computer problems.

United named Oscar Munoz as president and chief executive to replace Mr. Smisek. He is a member of the United board who previously ran the rail giant CSX.