Hank Krakowski offered his resignation to FAA Administrator Randy Babbitt, who said in a statement he accepted it.
"Over the last few weeks we have seen examples of unprofessional conduct on the part of a few individuals that have rightly caused the traveling public to question our ability to ensure their safety," Babbitt said. "This conduct must stop immediately. I am committed to maintaining the highest level of public confidence and that begins with strong leadership."
Babbitt called Krakowski a "dedicated aviation professional."
The FAA has been rocked by five reported instances this year when a controller apparently slept while on duty.
David Grizzle, FAA's chief counsel, was named as acting ATO chief operating officer while a search is conducted to permanently fill the position, Babbitt said.
The FAA administrator also pledged a top-to-bottom review of the air traffic control system.
"Employees at the FAA work diligently every day to run the safest air transportation system in the world," Babbitt said. "But I will continue to make whatever changes are necessary to ensure we concentrate on keeping the traveling public safe."
The FAA said Wednesday a second air traffic controller will be added to 27 control towers that currently have one controller on duty overnight. The change was effective immediately.
The decision followed an incident Wednesday in which a lone controller at Nevada's Reno-Tahoe International Airport fell asleep while a medical flight carrying an ill patient was trying to land, the FAA said.
The controller did not respond to radio calls for 16 minutes, and another control facility handled the flight's arrival, the FAA said. The controller was suspended while the agency investigates.