Though the government investigation into airline collusion is "not a huge surprise," it adds pressure to a sluggish sector that was "starting to bottom out," an airlines analyst said Wednesday.

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While a Department of Justice investigation and its fallout could affect carrier capacity moving forward, flight prices do not necessarily support possible collusion, said Joseph DeNardi, an airlines analyst at Stifel Nicolaus.

"To say that airlines are playing nice with one another because of consolidation is unfair to some extent," he said in a CNBC "Closing Bell" interview.

The DOJ confirmed Wednesday it was investigating whether airlines are colluding to grow at a slower pace to keep airfares high, and airline stocks slipped broadly lower on the news. The government has asked airlines for information as part of the investigation.

United Airlines said it had received a letter from the government and is complying with the investigation.

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DeNardi believes prices do not support price fixing. He noted that, adjusted for inflation, the average airfare has actually fallen 10 percent since 2000.

Still, the investigation will likely put pressure on the sector. Click here to see how airline stocks are faring.

—The Associated Press contributed to this report.