Japan's Emperor Naruhito received Egyptian President Abdel-Fattah El-Sisi at the Imperial Palace in Tokyo on Friday, a presidential spokesman said.
El-Sisi arrived in Japan on Monday to take part in the seventh Tokyo International Conference on African Development (TICAD).
The TICAD summit, co-chaired by Japan and Egypt, is being held in Yokohama from Wednesday to Friday.
Attendees include African leaders, and Japanese and Egyptian businessmen.
At the opening session, El-Sisi called on African countries and Japan to increase bilateral cooperation to benefit from Africa's natural resources.
As the current chairman of the African Union, the Egyptian president said he was hopeful the forum would achieve tangible results in furthering the partnership between Japan and Africa.
El-Sisi also met with Japanese Prime Minister Shinzo Abe on Wednesday to discuss enhancing cooperation between Egypt and Japan.