Japan's Emperor Naruhito and Empress Masako have spoken with dozens of Indonesians with links to Japan, following a meeting with Indonesia's president and his wife as part of a seven-day state visit.

On Monday, the couple met with about 60 people, including some who studied abroad in Japan and descendants of former soldiers of the Japanese army who remained in Indonesia after World War Two to fight for the country's independence.

The Emperor showed understanding of the hardships their ancestors had endured. The Empress expressed gratitude for the dedication of those who worked hard to build friendly relations between the countries.

Earlier in the day, they were welcomed to the presidential palace on the outskirts of Jakarta by President Joko Widodo and his wife. The Imperial couple also took a tour of a nearby botanical garden, escorted by the president and the first lady.

Joko thanked the Imperial couple for visiting Indonesia. The Emperor replied that he wishes to deepen his understanding of Indonesia's diversified society and culture, and reflect on the history of the country and of the people who have contributed to the friendship between Japan and Indonesia.

Afterward at the palace, the Emperor talked with the president, and the Empress with the first lady, before a luncheon hosted by the president and his wife.

During the talks with President Joko, the Emperor said it was exciting to head to the botanical garden in a golf cart driven by the president. Joko said it was the most nervous he has ever been as a driver.

On Tuesday morning, the Emperor and Empress are scheduled to visit Kalibata Heroes Cemetery. People who fought for Indonesia's independence from Dutch rule are buried there, including some of the former soldiers from Japan.