The inspection will take several days for each plane.
The certification process, Mr. Bofferding said, usually requires 50 engineers for each plane.
The agency estimated the inspection would cost $320 for each plane.
The cost for each plane has soared to $361 million, making it the most expensive fighter jet ever.
While the price for each plane is gradually coming down, Pentagon officials said it had not dropped quickly enough.
The design helped the carrier trim its costs by shaving a whole day in the painting cycle for each plane.
The argument can be made that the airport should charge a flat fee for each plane, regardless of size, which would encourage the airlines to use bigger planes.
Complicating the problem, aeronautical engineers write specifications for each plane, stating that pilots should not use the rudder above a certain speed, called "maneuvering speed".
The estimate includes a parts cost of $75,000 for each plane, and labor cost of $1,360, or 16 hours of work at $85 an hour.
She said her office was still refining the cost estimate, which equals $95 million to $113 million for each plane in current dollars.
That, in turn, would reduce their orders for the F-35, driving up the price for each plane and forcing them to cut orders further.
