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Have not visited this area but if you were going to Rome or say Athens you must go through the port access and for Athens it is Pireaus so it could be as simple as this.
I think that you ought to address this question to the agency or cruise line with whom you booked your cruise. This site seems in the main to be answered by passengers. However Manaus is a starting point for many of the cruises going the 1000 miles down the Amazon to to sea and is in itself an interesting city/town that has its own Opera House. Usually you are flown in via Miami or Rio and stay one night in a hotel on the outskirts. Brilliant place, fascinating area but beware of the sun as you are on the equator and the mosquitoes which are often small but bite like fury. There is a great deal you obviously will need to be told by the people with whom you booked so ring them, All the best Neil Dow.