The Federal Aviation Administration proposed the penalty totaling $1,005,000 after discovering evidence that the Seattle-based airline installed new security flight deck doors on the airplanes using blind rivets instead of the required solid rivets.
The FAA alleges that Horizon operated the 22 Bombardier turboprop aircraft on 186,189 revenue passenger flights between Dec.1, 2007, and June 1, 2011, before replacing the rivets.
The FAA also alleges the airline, even after being told the aircraft were not in compliance, operated one of the aircraft on another 22 passenger-carrying revenue flights before replacing the rivets.
The installation of blind rivets can damage other components, including wiring, the FAA says.
"We expect airlines to comply with all of our safety regulations and to correct safety defects promptly," said U.S. Transportation Secretary Ray LaHood.
The FAA discovered the alleged violations when Horizon incorrectly modified a 23rd aircraft with blind rivets, and the plane experienced an in-flight wiring damage incident during one flight.
Horizon has 30 days to respond to the agency.