Earlier this year, the ceiling opened in mid-air on a Southwest jet, but the FAA said that plane is not involved in the fine.
Federal regulators said Aviation Technical Services in Everett, Wash. improperly performed inspections and repairs on 44 Southwest Airlines planes.
From 2007 to 2009, Aviation Technical Services failed to fully inspect the Boeing 737-300s for metal fatigue and incorrectly installed fasteners in rivet holes that hold pieces of aircraft skin in place, the FAA said in a statement.
It's proposing a fine of $1.1 million.
Aviation Technical Services said in a statement that it is cooperating fully with the FAA and expressed confidence in the quality of the company's work.
The Associated Press contributed to this report.