Internal control is the priority to detect assets misuse, ensuring efficiency of operations andrnadherence to rules and regulation. Governments need an assurance whether the internal controlrnin their institutions is attaining these objectives. Audit reports of OFAG in recent years showedrnunfavorable audit findings on usage of budgets and compliance to rules and regulations in mostrnpublic universities. Thus this study focused on assessment of the effectiveness of the internalrncontrol system in the universities to identify the possible areas of deficiencies in the system. Thernstudy used cross sectional survey through questionnaires to employees of the universities andrnsemi structured interview with OFAG directors. Data were analyzed using descriptive statisticsrnand inferential statistics using SPSS results. The result indicates that internal control in thernuniversities is not effective. Particularly the risk assessment component of internal control is notrnpracticed in the universities. Though monitoring is better in the universities, there is in adequaterncontrol environment, control activities and inadequate flow of information and communication inrnthose universities.rnHence, it needs commitment from both universities management and responsible governmentrnauthorities to improve those specific areas of deficiencies’ in internal control indicated in thernfinal chapter of this study