An official from Japan's defence ministry said the country's planes regularly gather information on North Korea but declined to comment on the types of planes used or the locations monitored.
He spoke on condition of anonymity, citing government policy.
The threat against alleged Japanese aerial espionage is rare, though North Korea has regularly complained of US spy missions in its airspace.
Japan is very sensitive to North Korea's missile programmes, as its islands lie within easy range.
In 1998, a North Korean missile flew over Japan's main island. Tokyo has since spent billions of dollars on developing a missile shield with the United States and has launched a series of spy satellites primarily to watch developments in North Korea.
But in April, another rocket flew over Japan's main island, drawing a strong protest from Tokyo.
Pyongyang claims it put a satellite into orbit, while the US and its allies say it was really a test of the country's long-range missile technology.