United Continental ousted CEO Jeff Smisek Tuesday amid a probe into improprieties at the Port Authority of New York and New Jersey. Smisek, who was chairman, president and chief executive, will receive about $4.9 million as a separation payment.

United tapped Oscar Munoz to take over as CEO, effective immediately. In a letter to employees Tuesday, a copy of which was obtained by CNBC, Munoz said he planned to meet with staff to figure out how the company could operate better and improve customer service.

The airline previously disclosed an internal probe related to a federal investigation related to former Port Authority Chairman David Samson.

"We ... don't expect it to effect operations," Brett Hart, executive vice president and general counsel at United, said in a conference call, but declined to comment further.