The study objective was to assess the current status of HIV knowledge, attitudes and behavior (KAB) among employees of Namibian ministries. As most HIV campaigning takes place in the capital of Windhoek, an additional aim was to compare Windhoek to four regions (Hardap, Erongo, Oshana, and Caprivi). Between January and March 2011 a cross-sectional survey was conducted in two Namibian ministries, with participants selected randomly from the workforce. Data collection was based on questionnaires. 832 participants were included in the study (51.6% male). Nearly 90% of participants reported to have been tested for HIV before. Knowledge about HIV transmission ranged from 67% to 95% of correct answers, with few differences between the capital and regions. However, a knowledge gap regarding HIV transmission and prevention was seen. In particular, we found significantly lower knowledge regarding transmission from mother-to-child during pregnancy and higher rate of belief in a supernatural role in HIV transmission. In addition, despite many years of HIV prevention activities, a substantial proportion of employees had well-known HIV risk factors including multiple concurrent partnership rates (21%), intergenerational sex (19%), and lower testing rates for men (82% compared to women with 91%).