The train runs soley on litium ion batteries until it reaches 30 mph. The deisel engine then kicks on and provides the boost needed to get the train really moving, and re-charge the batteries, if needed. Of course, the train's breaking also recharges the batteries, and the engine automatically shuts off when the train is in idle.
The hybrid system reduces particulate and NOx emissions by around 60% and improves the overall efficiency of the train by around 10%. The Railway Company is also hoping that fuel batteries will become a viable alternative to fossil fuel engines, and has created the train with the specific intent of eventually replacing the deisel engine with fuel batteries.
From the Japan Times