The execution of management control system (MCS) in the public sector is very challenging mainly if these strategies come up from private sector. The strategic implementation of Management control system (MCS) is also a very big challenge for the public sector. This study is mainly intended to explore management control system practice and challenges in relation to efficiency. The main objective of the study was to study the effect of management control system (MCS) on employee's efficiency. The data was gathered through questionnaires and interviews and the study was employed in both quantitative and qualitative study approaches to analyse the MCS. The target population for the assessment was employees, officers, and managers in the study. A questionnaire was administered on the five Likert scales for which it was mainly used for the quantitative part, and semi-structured interview guide for the qualitative part was used as data collection tools. SPSS sofware was employed for statistical analysis. The total of 188 questionnaires was distributed to employees based on the sample size and the response rate of the survey is 95.3%.