Ferrari said the Frenchman, also the FIA's deputy race director for Formula One, would report to their technical director Mattia Binotto once at Maranello but did not state the role.
Mekies, a former chief engineer at Red Bull-owned Toro Rosso, is the second high-profile FIA official to join a team over the past year.
Marcin Budkowski, a Polish-born aerodynamicist who also previously worked for Ferrari and McLaren, has joined Renault F1 after resigning in September as the FIA's head of technical matters.
That move triggered criticism from rival teams who said it was unacceptable for someone in Budkowski's position, with access to secret information, to begin employment with a competitor after such a short hiatus.
The FIA said Mekies, who joined them in 2014, would continue to act as safety director across all championships until the end of June but would give up involvement in Formula One with immediate effect.
(Reporting by Alan Baldwin, editing by Ken Ferris)
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