"The F-35 fleet mission capable rate - the percentage of time the aircraft can perform one of its tasked missions - was about 55% in March 2023, far below program goals," the report said on Thursday.
The GAO called this level of operational readiness "unacceptably low."
"The program was behind schedule in establishing depot maintenance activities to conduct repairs. As a result, component repair times remained slow with over 10,000 waiting to be repaired - above desired levels," the report said.
Organizational-level maintenance has also been affected by a lack of technical data and training, the report added.
It will cost $1.3 trillion to keep the full F-35 fleet operational and flying even if or when all the repair and maintenance bottlenecks, as well as ongoing development problems with the aircraft's cannon, ejector seat, software and hardware are fixed, the report said.
However, despite the downfalls associated with the F-35 program, the report also determined that the Biden administration and the Department of Defense remain committed to a $1.7 trillion expenditure on buying a total of 2,500 F-35s for the US armed forces.
"In the coming decades, the Department of Defense plans to spend an estimated $1.7 trillion on nearly 2,500 F-35s," the report stated, acknowledging that the majority of the funds will go to operating, maintaining, and repairing the aircraft.
The F-35 aircraft now represents a growing portion of the Defense Department's tactical aviation fleet with about 450 of the aircraft fielded, the GAO said.