A Dissertation submitted to the Dare es Salaam Campus College in partial full fulfillment of the requirements of Masters of Science in Procurement and Supply Chain Management (Msc.PSCM) Degree of Mzumbe University.This study aimed at addressing the “challenges facing the public sector in customs clearance of imported goods through Sea Port and their impacts on the overall operations at the Medical Stores Department (MSD)” in Dar es salaam. The general objective of this research was to document the challenges facing the public sector in customs clearance of imported goods through Sea Port and their impacts on the overall operations, at the MSD. This research was designed as descriptive and diagnostic and was conducted as case study at the Medical Stores Department (MSD) in Dar Es Salaam. Non random sample of employees were chosen specifically judgmental sampling method was used, where by 20 respondents from clearing section were chosen by the researcher. In presenting and analyzing the data, both descriptive and analytical statistical methods were employed. The data collection methods during the study comprised of interviews, observations, questionnaires and documents examination. The main findings and analysis of the study was based on the data collected from questionnaires, documentary reviews and the interviews made during the study. In general among the findings were the Import clearance procedures in Tanzania being too long, complicated and not allowing timely delivery of goods to MSD. Lack of representatives from all key offices concerned in clearing procedures such as customs, regulatory authorities, shipping lines to the Port, hence necessitate individual office to be visited in separate occasions. Other findings were unscheduled deliveries of donors funded consignments appeared by 85%; small number of Clearing Officers by 90%, lack of push money (corruption) appeared by 95% and late payment of invoices for regulatory boards appeared by 85%. Firstly, the researcher is recommending to the MSD the following: It should increase the number of clearing staff from the currently twenty staffs to at least twenty five who can handle clearing of all goods procured by MSD as well as those procured by donors. The payment procedures of service invoices during clearing should be revised to reduce the time spent on effecting payment hence the speed for clearing of goods will be increased, approvals will be promptly obtained.