Where in Japan will you be?
Yes car factories in Japan have tours, some like the Toyota factory near Nagoya individuals can join into a tour and is in English and Japanese.
http://www.japan-guide.com/e/e3308.html
Other tours like Honda located near Hamamatsu only allow members who are part of a group of 10 or more.
Mazda in Hiroshima has a mix museum plus assembly line viewing:
http://www.mazda.com/about/museum/