A common problem in maritime transport is safety. More factors affect the safety of the ship, the people, the environment and property. These factors are the grounding, collision, fire, capsizing, failure of the main electricity, damage to the main hull, pollution and so on. The factor that is considered in this thesis are collisions which are considered respectively through this doctoral thesis on the real problems of maritime transport using appropriate software tools to improve safety navigation. International Maritime Organization - IMO seeks to implement new systems such as e-Navigation in shipping with a view to harmonize the use of advanced navigation systems . Disadvantages of such systems and technologies are reflected in the traffic crossing of sea passages where the passage width decreases and the traffic density increases. The goal of this doctoral thesis is to develop formal method for sinthesis of supervising system for controlling marine traffic in aquatoria with increased collision danger which would monitor and control marine traffic and restrict transition of ships between the sectors. The objective of installing a supervising system in the coastal center is to prevent collisions and to improve safety in dangerous sea passages. The supervising system would monitor the traffic of ships in the respective traffic crossing in a way to achieve an early warning of impending danger. The supervising system would track the route that ship receives from the coastal center, and in the event that the ship does not follow a fixed route, supervising system alerts operators at traffic control center and ship. The proposed supervising system would restrict moving of ships between sectors and coordinate the traffic of ships traffic crossing only in the event of high collision risk. This paper synthesizes the supervising system which controls the vessel traffic using Petri net and the P-invariant mathematical method. Verification of the supervising system is done by using computer simulations based on Petri net program ''Visual Object Net''.