Background Road trauma represents a major but neglected public health challenge in Malawi that requires concerted efforts for effective and sustainable prevention. In order to make the road traffic system safer, it is important to develop an understanding of the whole system and its elements including vehicles, roads and road-users along with their physical, social and environmental circumstances. In this study, we measured data quality in terms of database and variable completeness of road trauma case reports to determine if the data are sufficient for informing, monitoring and evaluating road safety interventions. Methods This was a quantitative retrospective study based in Ntcheu district, Malawi. Data were collected for year 2018 from both police and hospital sources. Categorical data exploration from these two sources was done using frequency distribution tables. Continuous data were summarized using means and standard deviation. Data source completeness was assessed using the capture–recapture methodology, while variable completeness was assessed using a checklist developed from the World Health Organization’s minimum injury surveillance core data set. Results The hospital data source was incomplete in areas of road user type, time of injury, mechanism of injury and place of injury. Thirteen case matches were identified between the two databases. Using the capture-recapture methods, the estimated road trauma events in Ntcheu district for the year 2018 is 954 (95% CI: 457, 1451) and an estimated 173 deaths (95% CI: 89, 257) in the same year. These estimates indicate 11% and 14% ascertainment of fatalities for the police and hospital data sources respectively.Discussion and conclusion There is significant underreporting for road deaths and injuries in Ntcheu district, which means there are critical data quality challenges in the respective data sources. It is therefore imperative for the road safety agencies and partners to resolve these data reporting and acquisition challenges.