They are trying to map the danger spots in one of the world's most earthquake-prone regions.
The scientists are triggering a chain of explosions along a line, about 550 kilometres (342 miles) south west of Tokyo.
The line bisects Japan's main island, from the Pacific Ocean to the Sea of Japan.
The study will analyse the structure of the Earth where two tectonic plates meet.
The movement of these rigid slabs of the Earth's crust are believed to be related to major earthquakes in the area, both on land and at sea.
Prediction dream
The seismological study - Japan's largest yet - is estimated to cost between 50 million and 100 million yen (421,000 to 844,000 dollars).
It is being carried out by the University of Tokyo and the Japan Marine Science and Technology Centre.
There is currently no way of predicting earthquakes with any accuracy in the short-term.
Geologists can only provide 30-year "hazard estimations" of an earthquake occurring on a particular fault in a certain area.
The scientists, led by Professor Takaya Iwasaki of the Earthquake Research Institute in Tokyo, hope the work will go some way towards realising this goal.