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When you travel in CBD Nagasaki, tram car and bus are good transportation.
Tram fare is 120 yen flat rate. Pay cash when you alight. Nagasaki Prefecture has its own smart card system which is not compatible with other card system such as JR Kyushu's Sugoca, JR East's Suica. The card is only compatible among the public transportation system (tram car and bus line) within Nagasaki Prefecture. The tram has 3 lines. When you transfer to other line, pay cash and the driver will give you transfer ticket. Put the ticket into the collection box when you alight afterwards. The tram has one day pass at 500 yen. The pass can be purchased at major hotels and the tourist information centre at JR Nagasaki station.
Nagasaki Bus has also one day pass at 500 yen. The pass can be purchased at the tourist information centre at JR Nagasaki station and Shinchi service centre.
When you drive to Nagasaki, you can't expect main tourist attractions in CBD, such as Glover Garden, to have its own car park. Park you car at Prefectural (Kenei) Parking at Oura Kaigan or Amu Plaza, and ride tram car or bus. If you visit outskirt, driving is still efficient. Iojima island is nice place to visit. On the northern suburb, drive R202, aka Sunset Road, onto Sotome area, where there're beautiful coast line and old churches. The view is really breath taking. You don't have to drive in Nagasaki.