Capt. Lee Moak told USA Today Tuesday that "we have a long way to go" before drones can share airspace with passenger jets.
Moak issued the warning in response to the U.S. Senate's passage Monday of legislation requiring the Federal Aviation Administration to come up with ways for drones to fly safely in U.S. skies in three years.
Proponents see all kinds of uses for drones from law enforcement to scientific.
"There is a huge potential market for civilian and commercial use of unmanned aircraft systems," said Ben Gielow, general counsel for the industry group Association for Unmanned Vehicle Systems International.
Despite their successful flights in Afghanistan, drones occasionally malfunction.
Last August, an unmanned Shadow drone collided with a C-130 cargo plane forcing the plane to make an emergency landing at a base in eastern Afghanistan, and in December a sophisticated U.S. RQ-170 Sentinel spy drone went down in eastern Iran.
In addition, the FAA doesn't certify drones like passenger planes against engine failure or wings falling off.
"You've got to find a way to apply today's technology to regulations that were written years ago," said former FAA chief Bobby Sturgell. "The message behind the legislation is 'Let's make this happen.'"