The ministry said the flights took place on December 22 and then again from December 24-26.
On December 25, Japanese media reported that Japan had sent F-15 aircraft in response to the sighting of the Chinese plane.
Japanese defense officials say the Y-12 propeller plane from China's State Oceanic Administration was spotted about 100 kilometers north of the uninhabited islands, known in Japan as Senkaku and in China as Diaoyu. After Japan scrambled fighter jets, the plane left the area.
The islands, which may sit on top of vast oil reserves, have been a source of major tension between the two Asian powers.