There is a lack of effective health information management systems in Nigeria due to the prevalence of cumbersome paper-based and disjointed health data management systems. This can make informed healthcare decision making difficult. This study examined the information technology (IT) skills, utilisation and training needs of Nigerian health information management professionals. We deployed a cross-sectional structured questionnaire to determine the IT skills and training needs of health information management professionals who have leadership roles in the nation's healthcare information systems (n=374). It was found that ownership of a computer, level of education and age were associated with knowledge and perception of IT. The vast majority of participants (98.8%) acknowledged the importance and relevance of IT in healthcare information systems and many expressed a desire for further IT training, especially in statistical analysis. Despite this, few (8.1 %) worked in settings where such systems operate and there exists an IT skill gap among these professionals which is not compatible with their roles in healthcare information systems. To rectify this anomaly they require continuing professional development education, especially in the areas of health IT. Government intervention in the provision of IT infrastructure in order to put into practice a computerised healthcare information system would therefore be a worthwhile undertaking.