Here's another one Henry:
http://www.sotozen-net.or.jp/kokusai/list/eiheiji.htmEiheiji Temple in Fukui is a centre of Japanese Zen Buddhism. This what is quoted on Wikipedia: "Visitors can apply to attend a two-day (sanrosha) or three-day (sanzensha) meditation training program at Eiheiji Monastery. Since the 3-day program is quite strenuous, applicants must have long Zazen (meditation) experience to gain admittance. While the program is advertised as 2 or 3 days, it is in fact less as the first day activities start 4PM with those on the final day ending at 10AM. During the full days there is 3:30AM wakeup until 9:30PM lights out. Gaining admission for the program requires faxed permission from the temple before arriving, and applications must be made at least a month in advance. There are several possible dates in any month for a stay.
It isn't always easy though. One guy I knew had to sit up straight for a long time while meditating. If he didn't the priest would belt him on the back with a piece of bamboo. Though, knowing this guy, he probably enjoyed it...

However, don't know if this is close to you. If not, you can ask around a lot when you get to Japan you might be able to find something a little more closer but still authentic, rather than something tailored towards tourists.