It is the first such incident to be announced by the ministry since China created its new air defence identification zone (ADIZ) in November last year, which has stoked tensions in the region.
The Chinese Y-12 propeller plane flew into Japan's own ADIZ, about 160 kilometres (99 miles) from airspace around the Tokyo-controlled Senkakus, which Beijing claims as the Diaoyus, the ministry said.
The aircraft headed back towards China without entering disputed airspace after Japan's military planes became airborne, a defence official said, without confirming further details.
China's ADIZ also covers the disputed islands.
The incident came amid diplomatic bickering between Japan and China, which descended into name-calling in the British press Monday.
Ambassadorial claim and counter-claim invoked the fictional evil wizard of the Harry Potter series, Lord Voldemort.
Japan's foreign minister Fumio Kishida left for Spain and France on Tuesday, where he was expected to press Tokyo's case in its spat with China.
Chinese government ships and planes have been seen off the disputed islands numerous times since Japan nationalised them in September 2012, sometimes within the 12 nautical-mile territorial zone.