“The departures announced today 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 company said in a statement. “The investigations are ongoing and the company continues to cooperate with the government.”

Though the resignations would appear to signal trouble for Mr. Samson, the authorities have given no sign that they were ready to bring charges in connection with the “chairman’s flight” arrangement and apparently did not know the executives were stepping down until Tuesday.

The resignations also complicate the fortunes of Mr. Christie, a Republican, as he moves ahead on his presidential bid, by underscoring the accusations of cronyism that have dogged his administration since the bridge scandal broke.

The governor has distanced himself from other figures implicated in the scandal, saying they had deceived him. But Mr. Samson, despite his resignation, has remained one of the governor’s closest advisers.

Several months ago, United asked the law firm Jenner & Block to conduct an internal investigation into the airline’s dealings with Mr. Samson and the Port Authority. At the time, lawyers close to the case predicted that it would lead to the resignation of Mr. Smisek and possibly other executives, in the hope that the airline could avoid prosecution.

Karen Kessler, a spokeswoman for Mr. Samson’s lawyers, said they had no new information about the federal investigation. She declined to say what it might mean for Mr. Samson. “This is a United matter,” she said.

United’s shares closed down 1.5 percent at $56.51 a share following the announcement on Tuesday. The stock has underperformed Delta Air Lines since the merger, as investors have become increasingly weary of United’s financial returns and operational record.