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An excellent place to run is on the grounds of the Imperial Palace. A high wall protects the palace grounds from the surrounding city. You can run a loop inside the wall that is about two kilometers or so. Beautiful surroundings. Once inside the wall you would never guess that you are in the center of a very large city. Several gates allow entry into the palace grounds. I ran during the day, and I am certain that it is a very safe place to run during daylight hours. I saw both locals and tourists running around the grounds. Avoid the traffic and have some fun, cars are not allowed on the palace grounds. I stayed at the Okura Hotel, accross the street from City Hall, and it is about one half kilometer from the palace grounds.