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Internal control system is a topical issue following global fraudulent financial reporting and accounting scandals in both developed and developing countries. The aim of this study is to investigate internal control system as a tool for achieving efficiency in the public sector using the Ministry of Education, Benin-city as a case study. The descriptive survey was used in the study with the aid of questionnaires. A sample size of 200 respondents were determined with the Taro Yamene formula. Structured question was used as the research instrument to collect primary data from respondents from the survey. Results from the study shows that majority of the student respondents were female (57.0%) while the females were represented by 43.3% were aged between 35 years and 40 years (30.0%) and married 47.0%. The ministry of Education, Benin city was used to study internal control as an aid to accountability in the public sector. In this study, internal control was seen to constitute the system adopted by establishments to protect the assets, to protect against improper asset disbursements, to protect against the incurrence of improper liabilities, to ensure the accuracy and dependability of all financial and operating information, to judge operating efficiency, to measure adherence to the government policies. A complete and integrated system of accounting should be established. It should be designed to create a clear accountability for the ministry operations and ensure the accuracy of the accounting records and financial statements. The accounting and operating procedures should be set forth in accounting and procedures manual, so that public sector policies and instructions may be clearly known and uniformly applied.