The study on how is Internal Control System developed in public institutions is of a special importance for modalities, forms and the manner of the application of relevant strategies for the functioning of internal control environment in public institutions. In this paper, there is treated the existing situation of internal control system environment of public finances and its implementation in public sector. For internal control system environment in public finances to function effectively, there should exist a coherent control environment which includes responsibilities for financial management from managers of Publicly Owned Enterprises and with complete functioning of internal audit, which exists in the function of development to add value. In Kosovo public institutions, this framework is offered by legislation and by institutional mechanism for the implementation of legislation according to these parameters.