Background Technological advances in clinical data capturing and storage systems have led to recent attempts at disease surveillance and region specific population health planning through regularly collected primary care administrative clinical data. However the accuracy and comprehensiveness of primary care health records remain questionable. Methods We aimed to explore the perceptions and experiences of general practice staff in maintaining accurate patient health data within clinical software used in primary care settings of regional NSW. Focus groups were conducted with general practitioners, practice nurses and practice administrative staff from 17 practices in the Illawarra-Shoalhaven region of the state of New South Wales (NSW) in Australia that had participated in the Sentinel Practices Data Sourcing (SPDS) project - a general practice based chronic disease surveillance and data quality improvement study. A total of 25 respondents that included 12 general practitioners (GPs) and 13 practice staff participated in the 6 focus groups. Focus groups were audio-recorded and transcribed verbatim. Thematic analysis of the data was undertaken. Results Five key themes emerged from the data. Firstly, the theme of resourcing data management raised issues of time constraints, the lack of a dedicated data management role and the importance of multidisciplinary involvement, including a data champion. The need for incentives was identified as being important to motivate ongoing commitment to maintaining data quality. However, quality of software packages, including coding issues and software limitations and information technology skills were seen as key barriers. The final theme provided insight into the lessons learnt from the project and the increased awareness of the importance of data quality amongst practice staff. Conclusion The move towards electronic methods of maintaining general practice patient records offers significant potential benefits in terms of both patient care and monitoring of health status and health needs within the community. However, this study has reinforced the importance of human factors in the maintenance of such datasets. To achieve optimal benefits of electronic health and medical records for patient care and for population health planning purposes, it is extremely essential to address the barriers that clinicians and other staff face in maintaining complete and correct primary care patient electronic health and medical information.