There are teacher imbalances in primary schools in the rural and the urban areas as well as among education districts in Malawi. The study investigated the implementation of teacher deployment policy of the Ministry of Education in primary schools by examining reasons behind teacher disparities and the challenges that the policy is facing in the implementation process. The investigation also involved diagnosis of suitable measures to be employed in order to tackle the challenges of the policy implementation. The study covered three education districts: Lilongwe Urban, Lilongwe Rural East and Lilongwe Rural West and it predominantly used qualitative method and the quantitative method mainly complimented the major method. The results of the study found that various challenges such as lack of strategies in teacher deployment, absence of established posts in primary schools, erratic recruitment of teachers by the Ministry of Education (MOE) for a period of ten years after 1994,poor living and working conditions of teachers particularly in the rural area, contributed to the problem of teacher imbalances in primary schools and achieving teacher balance between the rural and urban areas was a major challenge. Other challenges that contributed to poor implementation of teacher deployment policy include: political interference, inadequate financial and material resources at district level; and poor utilization of education data in the allocation of teachers to various schools. Generally teacher deployment in primary schools will remain a major challenge unless issues of teacher shortage, resources and teacher working conditions among other things are resolved.