Mt. Fuji is located in a tectonically unique area, but various aspects of the structure have not been fully explained. Here we show the results from a magnetotelluric survey across Mt. Fuji along a 70 km observation line. The profile shows that a conductive body is located between two resistive bodies at depths greater than 15 km. Low frequency earthquakes occur above the conductor. We interpret these results in a model where beneath Mt. Fuji, the subducting Philippine Sea Plate is split into two parts, and a magma chamber is located in the gap. Due to this unique structure, Mt. Fuji may be able to sustain a high basalt magma flux throughout its entire history.