A Dissertation Submitted to the School of Business in Fulfillment of the Requirements for Award of the Degree of Master of Science in Accounting and Finance (MSc A&F) of Mzumbe University.Many of the organizations’ activities are not attained due to poor or ineffective of internal controls system; with proper internal controls however guarantee the efficiency of a particular system (activities). Therefore, this study aimed at assessing the impact of internal controls on execution of payroll system to the Ministry of finance and economics affairs Zanzibar (MoFEA). The research methodology used case study research approach. A sample size of 60 respondents who comprised of MoFEA’s employees and other staffs working with the government of Zanzibar was involved. The methods of data collection involved both primary and secondary sources. Primary data were collected by using questionnaires and interview guide whereas documentary review was used in secondary method. The Statistical Package for Social Sciences (SPSS) software, and simple calculations by calculator were used to analyze the data where simple frequencies and percentages were created. The study findings observed that, internal controls were available on the payroll system of the organization; these were 78.3% of the respondents. Specifically 83.3% said that pay slips are issued, 65% segregation of duties is available, 95% block of salaries is exercised and 80% government payroll review is too exercised. Also the study revealed that some payroll activities were good enough for the efficiency of payroll system. In addition to that, it was found that there was compliance of internal controls in relation to the payroll system through punishments and having responsible parties to monitor the compliance. The study however portrayed that, almost 31.7% of the total respondents said that there were some weaknesses in relation to internal controls over payroll system. Following these results the researcher therefore calls for the Ministry to analyze and take the corrective measures with those weaknesses of internal controls over payroll system. The ministry also should pay salaries based on time (attendance) as this will discourage employees being absent from their work, independent check by the auditor and governments’ payroll review should be carried on in a scheduled manner. i.e. at a regular interval.