Been a few years since I was there but two places that I went to were Chofu Airport (west of Tokyo) - there are a few flying schools. Prices back in 1997 were around Y38,000 per hour for a 172
Another place was Honda Airport in Saitama (North West of Tokyo). They had 172's for around Y30,000 per hour.
Didn't end up flying there in the end, saved the money and flew twice as many hours back at home!..