President Rodrigo Duterte and his partner Cielito Avancena met Japan's Emperor Akihito and Empress Michiko on Tuesday at the Imperial Palace in Tokyo, discussing the at times strained history of relations between their countries.

According to the Imperial Household Agency, the meeting went on for around 25 minutes, during which the emperor noted that many local people lost their lives in World War II, when Japan occupied the Philippines for more than three years.

Duterte replied that the two countries have overcome their past to build cooperative ties, and expressed his gratitude for Japan's continued assistance in the postwar period.

A government source said the inclusion of a meeting with the imperial couple on Duterte's itinerary raised concerns among some in the Japanese government due to his history of controversial remarks.

But according to the agency, Duterte holds great respect for the imperial family and appeared nervous at the outset of his meeting with the emperor and empress, bowing to them as they came out to meet him.

• WATCH: Duterte finally meets Japanese imperial couple

Duterte had been tipped to meet the imperial couple for the first time during his visit to Japan in October last year, but the meeting was canceled following the death of Prince Mikasa, an uncle of Emperor Akihito.

On Monday, Duterte and Prime Minister Shinzo Abe held talks at which they affirmed their cooperation on regional issues, including North Korea and the South China Sea. They also released a joint statement laying out Japan's support for development projects in the Philippines over the next five years.