The aerodynamic coefficients are essential parameters to determine the flight performance of aircraft. They are estimated by wind tunnel tests and CFD analyses, and it is important to assess the validation by comparing those estimated from actual flight test data. In this comparison, uncertainties of estimated parameters are of strong interest, therefore the analysis of these uncertainties is a very important issue. In this paper, aerodynamic coefficients with their uncertainties are estimated from flight data, and their validation is implemented by the inverse simulation method. Then the causes of uncertainties are investigated and dominant causes are quantitatively identified. The aircraft weight has a dominant effect on CL, while the angle of attack and the thrust have a large effect on CD.