In recent years there has been a dramatic increase in acts of piracy at sea. In the age of globalization, piracy is not a trivial phenomenon - it is global organized crime which currently poses the largest threat to persons on board ships at seas and oceans throughout the world. According to the United Nations Convention on the Law of the Sea, a pirate's act is any act of voluntary participation and the use of a ship when the perpetrator knows that the ship has the characteristics of a pirate ship or an aircraft. Piracy is an act which is designed to encourage or intentionally facilitate acts as described in the Convention. In relation to this, there are ongoing discussions in the international community on the effective protection of ships against piracy attacks in the high risk areas. This doctoral thesis gives systematic analyses of effective models of preventive and timely protection of ships against potential piracy attacks, and in this respect provides the measures of ships defense against piracy attacks while sailing through pirate infested water and beyond. Based on research findings, there follows a proposal for a system of ship protection against potential piracy attacks by means of a Game Theory model conducted by the shipping company. Moreover, there are proposals for improvement of ship protection against piracy attacks by using simulations of different scenarios for attacks made by use of Petri nets.