As with any big project being implemented on such large scale and with a complex health care setting, a number of challenges arose.
District and regional administrative boundaries are frequently updated. The foundation of a new region generates a new representation of local population data. This disruption has an impact on the comparative analysis of HIS data such as the performance of health indicators.
Reducing the amount of existing standalone programs was often achieved through demonstrating the limitations of individual programs, and highlighting the potential of DHIS2. Due to some reservations however, some vertical programs are still running in parallel with DHIS2.
The lack of people with adequate HIS skills has at times weighed heavily on implementing and scaling up DHIS2 from a pilot region to the entire country. Tanzania has over 7000 health facilities across 168 district councils.