Prince William met with Emperor Akihito and his wife Empress Michiko at the Gosho imperial residence, bowing from the neck to both of them.
He arrived in a chauffeur driven car and was met by the royal couple outside the residence in Tokyo.
Addressing them in turn as "your majesty", the Prince told Akihito, who he last met in 2012 during the Queen's Diamond Jubilee Sovereign Monarchs' lunch: "Your majesty, it's very nice to see you again. Thank you for having me here - fantastic."
Prince William has called on China to unite with the United Kingdom in the fight against "ruthless" poaching and trafficking.
Relations between the Royal family and the Chinese have not always been friendly - but William's visit is helping build bridges.
The Duke of Cambridge became a fearsome samurai warlord - at least temporarily - when he visited the set of a long-running Japanese drama.