TOKYO—Every day, near a group of uninhabited islands in the East China Sea that have become the heated focus of dueling claims by Japan and China, dozens of Japan coast guard boats prominently patrol the waters, playing cat and mouse with Chinese surveillance vessels.

Some 1,200 miles away, in a roomy office overlooking warehouses and the busy Tokyo harbor, Akinori Saito does his own part to protect the waters claimed by Japan.

The...