Paris and Tokyo insist their relations are based on a "special partnership" rich in economic and military cooperation.
But the charges of alleged financial misconduct against Ghosn, who is a French national, have complicated the partnership since his initial arrest in November.
Abe held talks and lunch with Macron on the first stop of a major tour of Europe and North America to press the priorities of Japan's presidency of the G20 ahead of the Osaka summit in late June.
But the Ghosn case loomed large, with the business tycoon the subject of fresh charges on Monday in his fourth indictment.
Macron and Abe indicated that the case should not affect the strategic alliance between Renault and Nissan, which is backed up by a cross-shareholding and has existed since 1999, the Elysee Palace said.
The two leaders "reaffirmed their attachment to the Renault-Nissan alliance which is going to celebrate its 20th anniversary and is a major symbol of industrial cooperation between France and Japan," it said in a statement.
Presumption of innocence
In regards to the Ghosn case, France respected the independence of the Japanese judiciary but was "very vigilant concerning the respect of the rights and integrity of Mr Ghosn as a French citizen".
The Elysee emphasised that like any French citizen, Ghosn had a right to the presumption of innocence and consular protection.
A Japanese official did not immediately confirm if the Ghosn case had been raised at the talks but said it was up to the French side to bring it up.
Renault, Nissan and the third player in the alliance, Mitsubishi Motors, had in March created a new management structure headed by Renault Chairman Jean-Dominique Senard.
In a complex management structure, Renault - 15-percent of which is held by the French state - owns a 43-percent stake in Nissan.