Tokyo 2020 said it chose not to send the high-level delegation, which was originally set to include organizing committee president Yoshiro Mori and Olympics minister Seiko Hashimoto to Greece, due to the coronavirus.
Japan's ambassador to Greece will receive the flame at a handover ceremony, organisers said. Lower-level Tokyo 2020 officials who travelled to Greece last week will accompany the flame back to Japan.
Some 20 airline and airport staff waved the plane off with very little fanfare at the airport, which was almost empty as travel restrictions aimed at stopping the spread of the virus have lead to widespread flight cancellations.
Despite sporting events being cancelled across the world in response to the coronavirus outbreak, Olympics organizers maintain the Games will start as planned on July 24.