Steel pipes were found in grounds near the defence ministry.
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Police are investigating if two blasts near the defence ministry are linked to the sending of troops to Iraq.
A defence ministry official said there were no casualties or structural damage caused by the late-night explosion.
Police recovered batteries, timers and other materials from a nearby temple which may have been used to launch projectiles, reports said.
Officials say the blasts may have been set off by radicals opposed to sending Japanese soldiers to Iraq.
In January, Tokyo agreed to send troops to help rebuild Iraq in the first deployment of Japanese troops to a combat zone since World War II.
There are now 100 Japanese troops in a base in southern Iraq and more are scheduled to be sent to make a total deployment of 1,000 troops.
Critics have argued that the deployment violates Japan's pacifist constitution, but an opinion poll in a daily newspaper shows growing support for Prime Minister Junichiro Koizumi's decision.