Police say they have found evidence of two rocket-propelled bombs after two explosions were heard near a US naval base.
Local media reported that police were investigatng whether the blasts late on Friday were caused by an attempted attack on the Yokosuka Naval Base south of the capital Tokyo.
Residents reported that the roof of one home had been damaged by the blasts, police said.
Small, homemade rockets have previously been fired in protest against the deployment of US forces in Japan, but they have never caused any serious damage or injury.
The blasts occurred just hours after the US navy announced that the USS George Washington, a nuclear-powered aircraft carrier, was due to arrive on September 25.
It will be the first nuclear-powered aircraft carrier to be stationed in Japan, the only country to have suffered nuclear attacks.
Local residents and civic groups expressed concerns over the deployment of the USS George Washington after a fire onboard the warship in May.
Some Japanese living near the base are also opposed to the US military presence in Yokosuka and the increased number of American sailors the aircraft carrier would bring to the area.