You haven't said which cruise line you are using, but this is how Royal Caribbean handles it (excerpt from a larger answer):
"Requests for security clearance concerning late boarding or early departure must be submitted in writing to the Guest Flight Operations office for consideration at least one week prior to sail date. Guests must have a confirmed reservation in order to receive clearance. If the reservation was made by a travel agency, the agency must submit the request on travel agency letterhead. Guests with reservations made directly through Royal Caribbean International or royalcaribbean.com can submit their own request. Please include a return fax number or e-mail address.
If guests are pre-approved for boarding/departure in an alternate port of call, the ship's security staff is notified to expect the guests at the designated port. The approved guests are responsible for making all travel arrangements and will incur any additional expenses (for flights, hotels, transfers to the pier, etc.). Prepaid gratuities will be added to all approved reservations for the length of cruise.
Restrictions: Certain countries, such as the U.S., Italy and Norway, have cabotage laws affecting passenger movements. These laws restrict foreign flag passenger vessels (such as those operated by Royal Caribbean) from transporting guests from one port to another port in the same country. In the U.S., the cabotage law applicable to the cruise industry is commonly called the Jones Act but is legally titled the Passengers Services Act.
Please direct any requests and/or questions to the following e-mail address or fax number:
Fax Number: (305) 373-6695