Ocean Tokyu Ferry operates between Tokyo (Tokyo Ferry Terminal on Odaiba) and Kitakyusyu (in Kyusyu) VIA TOKUSHIMA. The ferry leaves Tokyo at 19:00 and arrives in Tokushima at 13:10 of the following day. I'm afraid but there's no English website for Ocean Tokyu Ferry. Reservation cam be made either at Tokyo Reservation Center in Tsukiji or by phonecall.
Tokyo Reservation Center: 7th Floor, Tsukiji MT building, 2-11-9 Tsukiji.
map (in Japanese): http://www.otf.jp/salesOffice/tokyo%20office%20map.pdf
Phone: 03-5148-0109
Ocean Tokyu Ferry (in Japanese): http://www.otf.jp/
This site may also help you.
http://www.interq.or.jp/white/ishiyama/e-column40-2.htm