There are air flights between Kagoshima domestic airport and some islands. There are ships connecting Kagoshima port (north pier) and each areas (A to C). Services may be delayed or canceled due to weather conditions. It is wise to check the website of the ferry company before traveling, especially in summertime when typhoons are common.
Most of these services do not operate daily, and some of them only run once or twice per week. In case of bad weather, you could be stranded on an island for over a week. It is better to arrange your itinerary allowing maximum flexibility.
all routes are Kagoshima - Yakushima
all routes are Kagoshima - Tanegashima
note:
*Ferries do not stop at uninhabited islands such as Gajajima, Kogajyajima.
*Tokara Islands can also be accessed by northbound TOSHIMA ferries from Amami-0shima (Naze port)
See detail info:
TOSHIMA VILLAGE OFFICE : ACCESS (Japanese)
http://www1.tokara.jp/contents/access/index.html
note:
Many of these islands have heliports, but they are reserved for emergency purposes (medical, press, etc.) only.
There are some ferry lines from Tokyo, Kobe, Osaka and Kagoshima to Naze port (Amami Oshima). And there are some local line from Amami oshima to other islands (Tokunoshima, Okinoerabujima, Kikaijima, Yoronjima).
See detail info:
AMAMI CITY OFFICE : ACCESS (Japanese)
http://www.city.amami.lg.jp/amami05/amami12.asp
Iwojima is under jurisdiction of the Japanese Ministry of Defense and inaccessible to the general public. However, when a total eclipse of the sun occurred near Ogasawara Islands on March 18, 1988, boat tours from Tokyo bay and Osaka bay were arranged.
It is likely that travel agencies will be offering similar tours for 2009 (we will post information as soon as we get any details).