The agency said in a statement late Wednesday that it had "found a potential risk [with the aircraft] that Boeing must mitigate. "
The 737 Max was grounded worldwide after a fatal crash of the plane in March. It was the second crash in five months for the aircraft model.
Shares of Boeing have been under pressure ever since.
A published report described the latest issue as computer system problem that could lead to the plane being pushed downward.
It was uncovered during simulations that were testing new software from Boeing for the plane, CNN reported, citing two unnamed sources.
Shares of Boeing fell $2.94, or 0.8% to $372 in after-hours trading.
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