Hiroyoshi Ichikawa, a Japanese police spokesman, said that he could not rule out a terrorist attack, and that suspected guerrillas, possibly leftist extremists, were likely to have been involved.
Leftist extremists have in the past used projectile launchers against targets in Japan related to the US military or on sites connected to the royal family.
The attacks are usually more symbolic than dangerous, and injuries or significant damage are rare.
The US has about 50,000 troops based in Japan under a security treaty.
Japan has stepped up anti-terror security measures around the country since the attacks on the United States on September 11, 2001.