The money was found in a plastic shopping bag, in a public toilet of the City Hall in Sakado, part of the commuter sprawl that surrounds Tokyo.
There was 10 million yen, wrapped up in neat bundles of notes, the equivalent of more than US$130,000 (RMB 830,570).
A handwritten message had been left with the cash and read: "I am all alone. Please let the people of Tohoku use it."
Tohoku is the northern region of Japan hit by the earthquake and tsunami in March.
City officials said the anonymous donor has slipped in and out unnoticed. If the money is not reclaimed within three months, they're planning to give it to the Japanese Red Cross.
Japan's great disaster brought out striking generosity and honesty in its people.
The equivalent of US$50 million (RMB 319,162,500) in cash picked up in the disaster zone has been turned in to the police.
Another US$30 million dollars (RMB 191,497,500) was recovered from safes found amid the rubble.