I would try to JASDF museum in Hamamatsu.

http://www.karo-aviation.nl/photo/pages/hama05.htm
http://forums.airshows.co.uk/viewtopic.php?f=10&p=193514

They have a Zero on display.

This list might help to find some others in japan though.

http://www.j-aircraft.com/misc/SURVIVE.HTM

Most of the Japanese warbirds I saw were displayed at the Udvar Hazy museum in Washington DC……:rolleyes: