Ships intending to fly the Maltese Flag must be registered with the Registry in the Merchant Shipping Directorate of the Malta Maritime Authority.

Registration takes place in two stages. The vessel is first "provisionally" registered and is issued with a Provisional Certificate of Registry, in terms of section 19 of the Merchant Shipping Act, valid, unless renewed, for a period of six months, and, upon satisfaction of certain requirements obtains full term registration.