Japan knows a massive flood is imminent. It is building defenses against it. However, Major floods in Australia have shown that even the most strategically placed levies can be "ignored" by rushing water.
Tokyo is encircled by rivers, with one running right through the middle of the city. The cost of such a disaster will be in the trillions. Despite calls for more spending by Toru Sueoka president of the Japanese Geotechnical Society there is a limit to how much can be spent to prevent destruction.
With enough water the rivers will rise to flood just about everything. Building the banks higher will do no good. Though other types of disasters are frequent, flooding causes more damage in the world than any other calamity, noting that flooding is a side effect of typhoons.