The agency said the investigation was looking into the issue in 2017 model year F-250 and F-350 Super Duty pickup trucks.
NHTSA will investigate to determine if the issue poses an unreasonable risk to safety and whether the agency should seek a recall.
In October 2017, Ford issued a technical service bulletin addressing the issue, and found water intrusion in the wire harness as the root cause of tailgate problems, NHTSA said.
A Ford spokeswoman said the company was cooperating with NHTSA in the investigation.
(Reporting by David Shepardson; Editing by Bernadette Baum)