A plane covered in Tokyo 2020 branding departed Haneda International Airport on Wednesday bound for Athens to collect the Olympic flame as organisers pressed ahead with plans.
A delegation, including organising committee president Yoshiro Mori and Olympics minister Seiko Hashimoto, was due to be on board but the decision was taken not to send them due to concerns over the coronavirus pandemic.
The flu-like virus has killed more than 7,500 people and brought sport to a standstill around the world.
Japan's ambassador to Greece will receive the flame at a handover ceremony, while Tokyo 2020 officials who travelled to Athens last week will accompany the flame back to Japan.
The torch relay in Greece last week was called off on the second day because crowds were too large, but organisers are determined to stage the Japanese leg of the relay despite the threat of the spreading the virus.
The Olympic flame is scheduled to travel the length of the country for four months from March 26 until the planned opening of the Olympics on July 24 at the national stadium in Tokyo.
Organising committee CEO Toshiro Muto said on Tuesday that a limited number will be allowed to gather on the roadside to watch the relay, but warned those displaying symptoms to stay away.
It comes after the International Olympic Committee on Tuesday reaffirmed their commitment to staging the Games on time, and ruled out any "drastic" decisions.
