Basically, there are four ways you can get to Yakushima using public transportation.
1. Fly with JAL Commuter Service.
Expensive, but fast and sometimes more reliable than sea travel.
Direct flights are offered daily to/from Osaka, Fukuoka, and Kagoshima. Folks flying from Tokyo can transfer in Kagoshima. Book 75 days in advance or look for campaign discounts for savings of over 50%. Transfers in Kagoshima are fairly hassle-free, and the Yakushima Airport is so tiny it feels more like a bus station. Most likely you'll fly on a DC8-Q400, which is a 74-seat prop plane that feels a lot smaller than it is. Although the planes are pretty reliable in rain and moderate wind, they cannot land in Yakushima if there is too much fog. (And you can't leave Yakushima until the plane you want to board lands!)
2. Skim across the water on a Toppy high-speed ferry (jetfoil).
|See my post about Jetfoils!|
As of writing, seats cost 16100 yen round-trip. Note that the schedule changes with the season, but the ride usually takes around two hours. Boats go to both the communities of Miyanoura and Anbo. You can also do a day-trip to the neighboring island of Tanegashima. The website is currently in Japanese, but try this link: http://www.yakushimatravel.com/ticket-english.html .Unfortunately, I cannot do it for you at this time unless you are booking a hike with me, but I do hope to offer this service, soon!
As a bonus, sometimes you can see flying fish if you crane your neck towards the rear of the craft. Because the jetfoil can travel straighter than the contour of the waves, you probably won't feel seasick unless the waves are several meters tall.
3. Stretch out on the Yakushima2 Ferry.
Cheap, easy, relaxing, but slow and not so reliable.
It's cheap (8900 yen as of writing), you don't (usually) need a reservation, and you can take lots of luggage, but the schedule doesn't fit everyone's needs, and the boat doesn't always run. The boat departs from Kagoshima at 8:30am and gets in to Miyanoura at 12:30. Then it departs again for Kagoshima at 13:30 and gets in around 17:40. The boat may be delayed or canceled in strong wind or waves. Sometimes it is docked for repairs for several days, so check the website.
You can relax in the lounge, order noodles, watch for flying fish from the deck, or even take a shower if you need to.
4. Travel like freight on the Ferry Hibiscus.
Dirt cheap, but it takes a long time, and it feels in no way like a passenger vessel.
First, you'll need to take a train to Saka no Ue Station and catch a taxi from the cab company next door to the station. There's a sign for the bus stop, but I don't see any sign of a bus. Also, bring food and bedding if you need it because the boat departs at 18:00 and gets in to Yakushima at 7am the next morning. You'll have some carpeted floor space to sit on in a room with a television, blankets, and mini-pillows, but that's all. From Yakushima it leaves at 8:20 and gets into the port near Kagoshima at 14:40. (You'll want to call a cab from there.) Cost is 3600 yen each way at time of writing. Keep in mind this is mostly a freight ferry, and it feels like it.
Perhaps even more importantly than getting to Yakushima, is leaving from Yakushima. Please keep in mind that flights and boats may be delayed or canceled due to weather. I strongly advise that you keep a buffer of several days before travelling internationally after you leave Yakushima. Also, if you go scuba-diving, you'll want to keep that in mind when booking flights, too.