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What ship and what port please?
If you are referring to a ship departing from a Mediterranean port, then the answer is yes. All you need to do is book a "cruise only" and make your own way to the port. However many cruiselines have airlinks arranged from various European countries, including Germany. The advantage of booking an air & cruise package with a cruiseline is that if anything goes wrong with the air travel, the cruiseline is responsible for getting you there by whatever means at their cost. If you book your own air travel, you are on your own.
If the ship is starting from the port in germany, Warnemunde? ask for a cruise only deal from the line and tell them you will be joining the ship at that port.
There are quite a few cruises leave from Amsterdam not far to get to on a cruise only option.