As a result of the mandatory implementation of European Union legislation into the Czech legal system is a significant change in the settings of the financial management and control in public administration. It is the acceptance of the principles of modern financial management and good governance. The aim of this paper is to point out the weaknesses of the current system of control of public resources management and state considerations de lege ferenda in order to increase the efficiency of financial control system.As a result of the mandatory implementation of European Union legislation into the Czech legal system is a significant change in the settings of the financial management and control in public administration. It is the acceptance of the principles of modern financial management and good governance. The aim of this paper is to point out the weaknesses of the current system of control of public resources management and state considerations de lege ferenda in order to increase the efficiency of financial control system