It said the Y-12 propeller plane did not enter airspace around the Tokyo-controlled islands known as the Senkakus, which Beijing claims as the Diaoyus.
The aircraft headed back towards China after Japan's military planes became airborne, defence officials said, declining to give further details.
The incident came as three Chinese government ships sailed into territorial waters around the islands, Japan's coastguard said.
The three marine surveillance ships entered the 12-nautical-mile territorial zone off Uotsuri island shortly after 7:00 am local time, the coastguard said in a statement.
It said the trio left the zone after just over two hours. Today's moves were the latest in a series by Chinese government ships since Tokyo nationalised three islands in the chain last September, reigniting the dispute.
They also came the day Japanese Prime Minister Shinzo Abe, speaking about the islands dispute, cited British former premier Margaret Thatcher and her thoughts on a 1982 war with Argentina over the Falkland Islands.