The epicenter of the earthquake was southern Chiba, about 60 km (35 miles) southeast of the capital, the prefecture where Trump is due to play golf on Sunday with Prime Minister Shinzo Abe.
No tsunami warning was issued and there were no immediate reports of damage from the quake which the U.S. Geological Survey measured as magnitude 5.
Trump and his wife, Melania, are due to arrive in Tokyo later in the day.