A Chinese aircraft was "confirmed to have violated the territorial airspace off the Danjo Islands in Nagasaki Prefecture," the ministry said in a statement, adding it had launched "fighter jets on an emergency basis".
The "Y-9 intelligence-gathering" aircraft entered Japanese airspace at 11:29 am (0229 GMT) for around two minutes, the ministry added.
Local media including public broadcaster NHK said the incident marked the first incursion by the Chinese military's aircraft into Japan's airspace.
Japanese and Chinese vessels have previously been involved in tense incidents in disputed areas, in particular the Senkaku islands in the East China Sea, known by Beijing as the Diaoyus.
The remote chain of islands have fuelled diplomatic tensions and been the scene of confrontations between Japanese coastguard vessels and Chinese fishing boats.
Beijing has grown more assertive about its claim to the islands in recent years, with Tokyo reporting the presence of Chinese coast guard vessels, a naval ship and even a nuclear-powered submarine.
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