Kumamoto Port is located about 12km from Kumamoto Station and is reachable by a shuttle bus that starts from the Kotsu Bus terminal, making one stop in front of Kumamoto Station and then non stop to the port.
The bus fare is 480 yen. There are more frequent regular city buses that go to the port but take 5 minutes longer..
There are two ferries running across to Shimabara from Kumamoto Port, the Ocean Arrow takes 30 minutes and costs 800 yen one way with a slight reduction if you buy a return ticket, and the slower Kyusho Ferry taking one hour and costing 680 yen one way.
This ferry in the video makes the short crossing from Kumamoto to Shimabara and back in Kyushu. The crossing takes one hour on the cheaper, slower boat run by Kyusho Ferry (Tel: 096 329 6111) or 30 minutes on the more expensive quicker boat operated by Kumamoto Ferry (Tel: 0957 63 8008).
Shimabara Port is about 3 kilometers from Shimabara Castle. There are a few buses that go to the castle, but more frequent buses go to the station which is a 10 minute walk from the castle. 5 minutes from the port is a station of the Shimabara Line which connects to Shimabara Station.
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