The necessity of the establishment of an internal control system for public sector came to agenda as much as private sector. The Republic of Turkey Law 5018 came into force determining the components for the establishment of internal cotrol system for public departments. This study aims to determine the univesities accounting units’ perception of the importance and current application levels of internal control system thus putting forth the difference , if there is between perception and application levels. New financial management and control law elements of system that fiscal transparency, accountability, accrual accounting, strategic planning and performance based budgeting, multi-year budgeting, internal control and internal audit has been regulated in Public Financial Management and Control Law No 5018. 55-56. Substance of the law no 5018 includes internal control. Important levels have made progress towards the establishment of the internal control system in public administration with published relating to internal control “Internal Control and Ex Ante Financial Control Procedures and Principles for Preregulation” and “Paper of the Public Internal Control Standards”. One of the basic constituent of the brand-new Turkish public finance management and control law whose administrative and juridical framework were determined in accordance with the law numbered 5018 can be said the foreseen internal control system which was designed in public administration and would be applied. An internal control system is required to be applied effectively in order to reach intended goals which are to run the activities of public administrations efficiently, in a productive and economic way. The goals and the basis of appointed politics of administrations stated in this definition are strategic plans of administrations. As stated in the definition, an internal control system includes all the activities and procedures of an administration so as to reach its objectives. These activities and procedures are financial or nonfinancial activities or procedures. Namely, an internal control is not limited to financial control in accordance with the law numbered 5018 The key role administrations to establish and apply the internal control system were given to top managers. The authority and responsibility of top managers are to form financial management and control system as predicted in the law, supervise the process, and take required precautions to observe and develop. The top manager would accomplish this task in cooperation with the managers of financial services, spending authorities and internal auditors and other officials. The law is enforced by directors of strategy development and spending authorities to establish internal control system in public administrations, to apply and develop no matter how the key role regarding internal control has been given to the top manager. However, it should not be forgotten that internal control is a process which every person from the very top executive to junior administrative officer has a role in various ways. Internal control system is an integrated system to reassure administration, internal and external shareholders in the fields of the efficiency and productivity of activities which are affected by board of directors, directors, internal auditors and officials, being accordance with related laws and regularizations, the credibility of financial reporting and reaching major corporate objectives. The sense of productivity growing in public administrations, becoming transparent and the need of accountability beginning with institutionalization, the increasing importance of corporate governance and performance necessitate the establishment of internal control system. In this study, the survey method was used to inquire how internal system was perceived by directorates of strategy development who play the greatest role in establishing, applying and improving internal control systems in state universities, and the present condition of accounting agencies in the head of departments. This survey study was carried out with the heads of departments who are the directorates of strategy development which is the accounting agency in universities. The number of universities which are within the scope of special budgeted administration as of the date of the performing the research in our country is 102. Though the number of universities as of the date of the performing the research was 102, the survey study was carried out in 94 universities. These universities could not be included since their presidents, and accordingly, directorates of strategy development were not assigned due to the fact that the institutional laws of one university were issued in the official gazette dated the 1st of April, 2010 and the institutional laws of seven universities were issued in the official gazette dated the 14th of July, 2010 when operations were being handled. In this study, it is aimed to reach the whole of the essential mass without sample selection; however, only 74 universities returned, which corresponds to 78,7 %, the rate of return. As a result of the survey study with the directorates of accounting agencies of 74 state universities, it is seen that the degree of perception of the directorates of strategy development regarding internal control system was high. The fivefold likert scale was used to measure the perceptions of head directorates. According to 20 statements measuring the degree of perception, the mean of the answers that head directorates was found to be 4.239. The closeness of the mean to the value “5” indicates the sensitivity of the directorates’ perception. That is, the directorates of accounting agency consider the establishment of internal control system as important. The statements measuring the degree of perception were adapted to present condition in order to compare the degree