With the decreasing college-aged population and the transforming policy environment in Japan, private universities are confronted with management crises, such as bankruptcy, mergers, etc. As the second largest source of funding, government subsidies for private universities is considered to have contributed to enhancing educational conditions and the soundness of financial management in the first two decades since its establishment but has a tenuous effect on the alleviation of students' economic burden. In this paper a statistical method is employed with the presupposition that private universities as a kind of organization rely on their external resources to make decisions. During the analysis, we have focused on the influence of government subsidies, with suppositions that there exist differences in government subsidy ratio among different types of private universities, and that in certain aspects government subsidy hinders private universities from achieving independence, and that the ratio increase of government subsidies should be favorable for alleviating students' economic burden. Through the analysis of financial data collected, we found that government subsidies did not show positive effects on promoting independence, and that its influence on alleviating students' economic burden proves to be complicated as correlation coefficients of government subsidy ratio and tuition & fees per capita, and No.3 Capital Fund which is considered to be prepared for research and scholarship, are negative. Such results show that regulations accompanied with subsidies are constrictive to private universities to some degree. However, besides the financial status, there are several other factors to consider when discussing management behavior of individual private universities, such as the higher education market, policy issues, and internal governance. In brief, government subsidies have complicated influences on private universities and such complication reflects these uncertainties. (Contains 12 notes and 7 tables.)