With increasing aquaculture intensification, emergence of fish health challenges is expected, hence, a country-wide baseline survey was conducted to explore the fish health challenges in fish hatcheries. This was done using a face-to-face questionnaire where 48% of the 56 visited hatcheries had experienced fish disease incidences, with the African catfish being the most affected species (81.5%). Disease signs and symptoms were mainly observed during the larva (51.9%), the fry (66.7%), fingerling (55.6%), and larva (51.9%) stage. Among 27 hatcheries, the most common disease signs and symptoms observed were cotton-wool growth (20), red spots on skin and fins (12), fish swimming upside down (12), and tail and fin rot (11). The analysis revealed that both the experience level of the farmer and the type of hatchery facility exhibited significant associations with disease signs and symptoms in hatcheries, with p-values of 0.0134 and 0.008, respectively. Most (65%) hatcheries monitored water quality. The majority (66.1%) of the hatcheries released their hatchery effluents directly into the natural waterways without prior treatment. These findings provide a benchmark to improve management strategies for increased survival rates and production in hatcheries.