Background: Staff absenteeism is a global challenge in health care service delivery that has not spared any country. Aim: This was to assess the factors contributing to staff absenteeism in public health facilities in Bushenyi District of Uganda. Method: This was a cross sectional study conducted for a period of 3 months in which data were collected using a questionnaire and interviews. Results: Majority of participants were females (66.4%) which 50% in the age of 31 -45 years. The study showed that residing outside the health facility (42.1%) i.e. walking distances over 10 km to get to work was a challenge.Family conflicts, overstay in one workstation without rotations to other major health facilities and drug abuse as well as inadequate supervision were major contributing factors to absenteeism (P < 0.05). This is complicated by increased administrative duties coupled with poor enumeration and motivation in the health facilities visited. However over 50% of the participants reported never to have left their work stations without permission, thus showing that the challenges faced in a majority of health centers in rural communities warrant national support through improved motivation of staff working in the challenging communities. Conclusion: Staff absenteeism in rural communities is a major challenge that needs a multi-sectorial approach for its effective management, thus showing a need to revise policy in the health sector.