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I travelled with fred olsen to fjords last august - it was great. We didn't book any excursions. you can book on board. did Bergen on foot easily - good bus that takes you to cablecar, up and back for fixed price - good value. went to tourist board quick on arrival in places and got local taxi/minibus to a few places - teamed up with other independent travellers. saw lots just by pottering.
If going to Flam the railway is at the dockside and so is the booking office. Ships charge about £20 a person more for the same trip, but may throw in a snack. The only problem may be is if more than one ship is docked, some trains may be full.