Abstract Background Developing countries participating in the mitigation mechanism of reducing emissions from deforestation and forest degradation (REDD+), are required to establish a forest reference emission level (FREL), if they wish to seek financial support to reduce carbon emissions from deforestation and forest degradation. However, establishment of FREL relies heavily on the accurate estimates of carbon stock as one of the input variable for computation of the emission factors (EFs). The product of an EF and activity data, such as the area of deforestation, results in the total emissions needed for establishment of FREL. This study presents the carbon stock estimates for different land cover classes based on an analysis of Tanzania’s national forest inventory data generated through the National Forest Resources Monitoring and Assessment (NAFORMA). Results Carbon stocks were estimated in three carbon pools, namely aboveground, belowground, and deadwood for each of the three land cover classes (i.e. Forest, non-forest, and wetland). The weighted average carbon stock was 33.35 t C ha−1 for forest land, 4.28 t ha−1 for wetland and 5.81 t ha−1 for non-forest land. The uncertainty values were 0.9% for forest land, 11.3% for wetland and 1.8% for non-forest land. Average carbon stocks for land cover sub-classes, which make up the above mentioned major land cover classes, are also presented in our study. Conclusions The values presented in this paper correspond to IPCC tier 3 and can be used for carbon estimation at the national scale for the respective major primary vegetation type for various purposes including REDD+. However, if local based estimates values are needed, the use of auxiliary data to enhance the precision of the area of interest is recommended.