Yes: the Tokyo network run by Soviet intelligence officer Richard Sorge — one of the most successful Soviet agents of that era — included native Japanese agents: the artist Yotoku Miyagi and the Asahi Shinbun journalist (and Japanese government adviser) Hotsumi Ozaki. Both men were communists, and supplied information to the Soviet Union on Japanese military planning and political sentiment towards Russia.

The intelligence Sorge et al supplied was of incalculable value to the Soviets — not that they reliably exploited it. The most notorious example is the fact that Moscow was warned of Germany's plans to launch Operation Barbarossa in 1941, and did not act on that intelligence.

Sorge's network operated from 1933-1941, when it was rolled up by the Kempeitai. Miyagi died in prison in 1943. Sorge and Ozaki were executed by the Japanese in 1944.

Check out Stalin's Spy: Richard Sorge and the Tokyo Espionage Ring by Robert Whymant; on Ozaki specifically, look at An Instance of Treason: Ozaki Hotsumi and the Sorge Spy Ring by Chalmers Johnson.

I've wondered about this before, and read a bit around it — it does appear that there were substantially fewer human intelligence operations carried out by the Allies against Japan than by the Japanese against the Allies. I'm not entirely clear why, but I suspect it has to do with the difficulty for western intelligence services of recruiting agents who can operate covertly in a very different, at the time very poorly-understood culture.

There were limited efforts to by the US military to recruit counterintelligence operatives from among the Nisei (second generation Japanese-Americans), but according to this page only two were recruited — and they didn't operate in mainland Japan but rather in occupied territories and behind the lines.

Edit: syntax / Edit 2: new link