The problem was discovered during what the Pentagon called a routine inspection at Edwards Air Force Base, California, of an Air Force version of the F-35. Other versions of the F-35 are flown by the Navy and the Marine Corps.
All versions were grounded on Friday.
The F-35 is the Pentagon's most expensive weapons program at a total estimated cost of nearly $US400 billion ($A392.50 billion).
The suspension of flight operations will remain in effect until an investigation of the problem's root cause is determined.
The Pentagon said the engine in which the problem was discovered was being shipped to a Pratt & Whitney facility for more thorough evaluation.