"Japan hopes that Iran's new president Ahmadinejad will continue to implement domestic reforms and respond to the nuclear problem by valuing relations with the international community," the foreign ministry said in a statement.
"Japan hopes that our traditional friendly relations will progress and expand further," the statement said, adding Tokyo enjoyed political, economic and cultural exchanges with Tehran.
On Saturday, hardline Tehran mayor Ahmadinejad swept to a shock landslide victory in Iran's presidential election against his moderate rival Akbar Hashemi Rafsanjani.
Some observers say the victory of Ahmadinejad, a self-proclaimed fundamentalist seeking a return to the moral "purity" of the early years of the Islamic revolution, could set the Islamic republic on a collision course with the West.
Iran claims its nuclear activity is purely non-military and that it has the right to enrich uranium for peaceful purposes, but Washington says Tehran is using its civilian program to mask covert atomic weapons work.
Iran accounts for 16 percent of Japan's total oil imports after Saudi Arabia and the United Arab Emirates. Japan has continued buying oil from Iran even after the Islamic Revolution in 1979 and the Iran-Iraq War of 1980-1988 and despite a US embargo.