In order to analyze the organizational performance of government-funded research institutes, four independent variables (organization size, organization age, evaluation system, organization location) and goal ambiguity were empirically analyzed. Although there are existing studies on institutional evaluation, which is the organizational performance of government-funded research institutes, there are differences in research in that it is an empirical analysis analyzed from the perspective of goal ambiguity and that the evaluation system, which is the specificity of institutional evaluation, is included in the analysis. As a result of the analysis, organizational location was the only independent variable that had a direct significant effect on organizational performance, and goal ambiguity showed a significant mediating effect for all independent variables. This indicates that goal ambiguity plays an important role in the organizational performance of government-funded research institutes, and to reduce this, increase the size of the organization, pay attention to establishment of the organization for organizational age, and that it is desirable to have an independent research group in the government department for the organization location. In addition, it was supported that the improvement effect of the evaluation system is proceeding in a desirable direction in terms of goal ambiguity.