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Go to the marina office first and tell them you need to check in. You don't have to be moored in the marina, can be anchored in the bay. The port authority is in the next to the marina office.
Boats entering from outside the EU will have to go to Corfu town for immigration control.
Cost 2018: 51.20 euro in the marina office and 15 euro to the port police office. Cash only.
Cruisers report it is a very quick and easy check-in.