Macron became the second foreign leader to be received by Emperor Naruhito since he ascended the throne on May 1, after US President Donald Trump and his wife Melania met him last month, reports Efe news.
Macron and the First lady visited the palace on the second day of their four-day Japan trip, after seeing the National Museum of Emerging Science and Innovation.
The couple attended a lunch with the Imperial couple and other members of their family, including their nieces Princesses Mako and Kako.
Official luncheons with foreign guests were discontinued in the palace in 2016 to reduce the burden on then-emperor Akihito, 85, but the practice has been resumed after he abdicated in favour of his son.
This was the second encounter between Macron and Naruhito in less than an year, after the latter met the French president in September 2018 during a France visit to mark the 160th anniversary of diplomatic relations between the two countries.
After the lunch, Macron and his wife headed to Kyoto where they are set to meet famed kimono maker Kunihiko Moriguchi - considered a national treasure in the Asian nation - as well as visiting the gardens of a well-known temple of the city and then dining with Japanese architects before leaving for Osaka.
On Friday and Saturday, Macron is set to participate in the annual G20 summit to discuss international trade, measures to fight plastic pollution as well as participate in efforts to stop the growing trend of trade protectionism kicked off by countries such as the US.
( With inputs from IANS )