In Uganda the first topi population counts in the Ishasha Flats region in the Rukungiri District, a part of Queen Elizabeth National Park, where the topi seemed to congregate, were calculated from monthly ground count samples from 1963-1967, but these were soon doubted as the methodology used caused an overestimation due to the spatial distribution of the antelopes in aggregations. Based on three ground-based counts in 1970, Jewell estimated a total of 4,000 topi in this area using a different calculation method. The mean population derived from estimations based on aerial surveys made in 1971 and 1972 was 4,932. Yoaciel counted a maximum of 5,578 in 1975, but in 1977 the numbers declined to half that, with the last count of 1978 jumping back to 2,973. At the same time, the home range of the population shrunk and kob numbers doubled. In 1981 a conservationist claimed that the Yoaciel et al. study revealed topi numbers here were 20% of their 1973 level in 1980, although that appears to be a incorrect. To explain the population reduction, Yoaciel et al. pointed to three causes: poaching pressure, lion predation and changes in the vegetation structure. Poaching had increased, especially with the establishment of a military border post in Ishasha. Lions in Ishasha had a preference for topi, in some years the topi formed over 80% of their prey, meaning the 32 adult lions roughly killed some 660 topi in those years, although lower percentages of topi prey in later years meant lions killed 320 a year. Lastly, the rangeland was changing in vegetation structure, with the tree species Acacia sieberiana encroaching upon the shrinking grassland. It was suspected either changed fire regimes and the local reduction in the elephant population due to ivory poaching was causing this afforestation. East estimated a that there were 580 individuals in 1998 in Uganda, with an unknown number in the Democratic Republic of the Congo (DRC). Joint aerial surveys of the adjoining Queen Elizabeth National Park, Kigezi Game Reserve and Kyambura Game Reserve in Uganda, and Parc National des Virunga (Virunga National Park) in the DRC, which together completely encircle Lake Edward, found that all of the topi cluster to the south of the lake shore in the Ishasha Flats. The total minimum population in this region was counted as 2,874 in the 2006 survey, but dropped to 1,302 in the 2010 survey. Another joint survey in 2014 found 2,679 topi in the region, most in the Uganda part. In 2020, Uganda Wildlife Authority executive director Samuel John Mwandha stated that the wildlife in park has been increasing in the last five years.
In the adjoining Pian-Upe, Bokora and Matheniko Game Reserves, and the controlled hunting areas surrounding and connecting these areas to Kidepo Valley National Park, topi were numerous in the 1960s. A ground-based survey in April 2012 registered no sightings of topi, it is possible they have been extirpated. The Uganda Wildlife Authority was planning to relocate twenty topi to the area as of 2013.