- There are birds that destroy the growing rice
- Use of poor farming methods outside the stipulated guidelines.
- Sometime R. Manafa over floods its valley during rainy seasons resulting in the destruction of rice fields.
- Bilharzia is a common disease on the scheme which attacks the local farmers.
- Competition for market with other foreign countries which produce and import rice into Uganda like Pakistan.
- Price fluctuation for rice both domestic and on international scene and this leads to losses.
- Limited capital to invest in growing of rice and carrying out irrigation.
- The canals usually silt which blocks the water transfer system.