The French leader was due to hold talks with Prime Minister Shinzo Abe Wednesday before meeting Japan's newly enthroned Emperor Naruhito.
Macron is only the second foreign leader to meet Naruhito, who took the throne last month after his father abdicated.
Abe and Macron have stressed that their ties remain strong despite tensions over the arrest of Ghosn, who once led an alliance of Japan's Nissan and Mitsubishi Motors and France's Renault.
But profound differences remain over how that auto partnership should evolve, with Renault seeking closer integration with Nissan, and the Japanese firm resisting.
Shareholders are still up in arms over the financial misconduct issues that have rocked the firm’s French partner, Renault.
Ahead of the trip, the Elysee Palace said Macron would emphasise "France's strong attachment to the (auto) alliance", adding that he hopes to hear support from Japan and Nissan for "the continuation and consolidation of this alliance".
Paris' desire to save Renault's alliance with Nissan--the French state holds a 15-percent stake in the auto company--saw it scupper talks between Renault and Fiat Chrysler for a potential merger -- a plan that was received cooly by Nissan.
Staying mum on Ghosn case
Macron is likely however to stay mum on the specifics of the case against Ghosn, who is out on bail in Tokyo under strict conditions as he prepares for trial on four charges of financial misconduct.
A lawyer for Ghosn urged the French leader ahead of his trip to raise human rights issues with Abe, after criticism over the lengthy pre-trial detention of the former auto executive, and the strict conditions of his bail.
The Japanese and French leaders will also be looking to co-ordinate on the major international issues that are set to dominate this week's G20.
Both Japan and France, which will chair a G7 meeting in August, back multilateral solutions to the major international crises of the day: the US-China trade war that is weighing on the global economy and tensions with Iran that risk spiralling into a Middle East conflict.
Abe earlier this month met Iranian leaders in Tehran in a bid to serve as mediator with Washington, but there has been little sign of a rapprochement, with Iran pledging to step back further from a nuclear deal from which Washington has already withdrawn.