The head of the air traffic controllers' union said Wednesday that it could take the industry "weeks to recover" from the impacts of the government shutdown .

Nick Daniels, president of the National Air Traffic Controllers Association, said on CNBC's " Squawk Box " that the holiday season will be especially affected by the shortage of air traffic controllers, who missed their first full paycheck last week. The Department of Transportation has reported increased delays and ground stops as a result of the shutdown, now in its fifth consecutive week.

"To somehow fathom we could go into the holiday season still in a government shutdown, I can't even begin to predict what the impacts will be across this country," Daniels said. "Three-hour TSA wait lines will be the least of our worries.

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