It is interesting to me that in this day and age few of the literary agencies have websites. They do, of course, have email. Please see the FAQ on the SCBWI Japan page for contact information for the literary agents. That page is meant for children's literature authors/translators, but I believe the agencies are the same.
There are 2 important lists on this site: authors out of copyright, authors they represent. There is also a form you can fill out to ask about translation permission (see number 17)
The Tuttle-Mori Agency is the oldest established, and biggest literary agency in Japan -- accounting for approximately 60% of the market....The company is also active in the licensing of Japanese works abroad, in areas such as the licensing of Japanese manga translation rights to over 20 countries around the world, as well as in the licensing of movie adaptation rights to both Japanese and western works.
Asano Agency
Asano Agency Inc.
Kiyoshi Asano
kiyoshi@asano-agency.com
