Mercury levels of Nile perch fillets to be exported from selected fish processing industries in Uganda were determined by hot digestion in strong acids, followed by analysing the extracts with Inductive Coupled Plasma-Mass Spectroscopy (ICP-MS). There was a clear link between atmospheric mercury and methylmercury accumulation in fish tissues, thus exposing a possible threat for human health. A quantitative cross-sectional study design was undertaken from two fish processing factories around Kampala city. Simple random sampling was utilised where ten fish products were picked for analysis. The results obtained from the analysis of samples from both factories presented mercury levels far below the FAO/WHO guideline level of 0.5 mg/kg for mercury in fish. The mercury levels for both factories were higher than the oral daily recommended dose of 0.001 mg/kg body weight for the vulnerable population raising eyebrows for the general population, since fish is a major contributor to mercury intake for consumers.