Macron and his wife, Brigitte, hosted an official dinner for Naruhito, who began a nine-day goodwill visit to France over the weekend. The dinner marked a showpiece moment of the prince's trip.
During a pre-dinner speech dwelling on the dense web of connections and history that tie France and Japan, Macron said hosting the prince at Versailles showed the "respect, esteem and friendship we have for Japan."
Macron recalled previous visits made to France by the prince's father, Emperor Akihito.
"France hasn't forgotten, just as it won't forget your visit," he said.
Macron and Naruhito also attended a theater performance at the glittering palace west of Paris.
The 58-year-old prince will inherit Japan's Chrysanthemum throne when the 84-year-old emperor abdicates next year.
Naruhito's visit marks 160 years of diplomatic relations between France and Japan.