The main aim in the adoption of automation technologies of airplanes is to decrease the errors due to human factors whereas some applications and empirical researches showed that automation causes new type of errors in the cockpit. When the aviation accidents due to automation have been surveyed, it is seen that the automation errors related to FMS (Flight Management System) are very high. The FMS supports pilots in different tasks like flight planning, navigation, performance management and monitoring of flight progress. In this study, the effect of automation and FMS in flight safety is researched. A survey was conducted to a group of pilots of a turboprop airplane with high level automation. Following the survey, an experimental study was performed to analyze effects of last minute changes on FMS which was highlighted as the most prominent problem in the survey. Finally, based on the results of experiment, recommendations were given so as to improve design and usability of FMS.