Employee motivation affects productivity and need to be channeled towards the accomplishment of organizational goals. A cross sectional study was conducted among Public Health Specialists (PHS) in the Ministry of Health Malaysia to study their motivation level and the factors influencing this. The respondents were from the Association of Public Health Specialists of Malaysia working in the Ministry of Health. Quantitative Technique self-administered questionnaires were used in this study and the questionnaires were mailed to the respondents. The response rate for this study was 72.3%. In measuring the motivation level, five (5) aspects were studied. The social aspect, self -achievement aspect and autonomy aspect were found to be the main aspects that motivated the respondents. With regard to motivation level, 55.8 % respondents had low motivation level. In order to improve the motivation level among PHS, the aspect of self actualization and autonomy required serious attention. In the future, PHS are expected to play a major role in controlling, promoting, preventing, maintaining, restoring and solving problems in order to enhance the health of the Malaysian population.