The paper was adopted by PM Shinzo Abe at a cabinet meeting on Tuesday.
It described China’s declaration of an air defence identification zone over disputed East China Sea islands as a “profoundly dangerous act”.
China’s actions, it warned, could result in “unintended consequences”.
China and Japan are locked in a bitter dispute over an island chain called Senkaku in Japan and Diaoyu in China. Japan controls the islands.
Since the row escalated, Chinese ships and planes have been moving in and out of what Japan says is its territory, leading to fears of a clash.