Delta Air Lines expects to have a strong fourth quarter despite flight disruptions caused by the federal government shutdown, the carrier's CEO Ed Bastian told CNBC Wednesday.

Bastian said that while the disruptions would cost a significant amount to the industry and the economy, they would not "wipe out" Delta's quarterly profits.

His comments follow a wave of flight cancellations by U.S. carriers over the past week caused by air traffic control absences.

Delta said its operation recovered from disruptions over the weekend caused by air traffic controllers' staffing snags coupled with seasonal weather in Atlanta and other areas of the country.

The shutdown, the longest in U.S. history, has forced 13,000 air traffic controllers and 50,000 Transportation Security Administration agents to work without pay.

Flight cancellations, however, sharply fell on Wednesday, hours before the House of Representatives votes on a bill to end a record-setting government shutdown.