Ship engine room has a structure which has to meet a number of needs with regard to administrative conditions. Therefore, when the complicated structure of engine room are considered, even a simple mechanical failure, if no measures taken abruptly, grows into irreversible condition, causing losses that cannot be compensated. A well-qualified ship engine conductor along with an effective error detection system is needed to detect failure and act immediately against any engine impairments possible. This study aims to manage troubleshooting in main engine auxiliary systems which cover cooling, lubricating and cooling oil and fuel systems. The study is also thought to be a good reference for maintenance processes for marine engineering operators. Breakdown of main engine equipment are examined and troubles hooting program is developed for using Fuzzy Analytic Hierarchy Process (F-AHP) determine solution methods and causes of such breakdowns. In this paper, a fuzzy Multi Criteria Decision Making (MCDM) methodology was proposed to determine the most effected system of the ship main diesel engine. The results showed that fuel system was the most effected alternative, as being followed subsequently by cooling system, governor system, air supply system and oiling system. The results were based upon the opinions of three experts groups who ranked the ship main diesel engine systems alternatives according to twenty-nine criteria expert selected.