The comments appeared in an annual defence white paper approved by Prime Minister Shinzo Abe's cabinet, with the report heaping criticism on Beijing's unilateral declaration of an Air Defence Identification Zone (ADIZ) late last year.
The ADIZ -- which overlaps on territory claimed by Japan -- sparked regional criticism as well as condemnation from Washington, while commentators have voiced concern over the possibility of an armed conflict between the Asian powers.
"Japan is deeply concerned about the establishment of 'the East China Sea ADIZ' which is a profoundly dangerous act that... Escalates the situation and may cause unintended consequences" in the region, the 505-page paper said.
The zone required aircraft flying through China's zone to identify themselves and maintain communication with authorities, but it was not a claim of sovereignty.
Chinese vessels and aircraft have regularly approached an East China Sea archipelago claimed by both countries after Tokyo nationalised some of the chain in 2012.
In a confrontation earlier this year, Tokyo said that two Chinese fighter jets flew within 30 metres of its aircraft in an area where the nations' air defence zones overlap.
Beijing responded that it was Japanese military planes that flew dangerously close to its aircraft.
Several Southeast Asian nations are also at loggerheads with China over separate territorial disputes in the South China Sea.
Relations between China and Vietnam plunged to their lowest point in decades when Beijing moved an oil rig into contested waters in early May, triggering deadly riots in Vietnam.
"These measures include dangerous acts that could cause unintended consequences and they raise concerns over China's future direction," it added.
In its initial response, China accused Japan of making "groundless accusations".
"Japan... Is deliberately creating a 'Chinese threat' as an excuse to adjust its military policy, and expand its manufacture of arms. China is firmly opposed to this," the defence ministry said in a statement on its website.
The paper, which is an assessment of Japan's thinking on defence matters, also warned that an unpredictable North Korea "repeatedly uses militarily provocative words and actions".
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