In both Mozambique and Tanzania farmer-led development of irrigation is widespread, yet it is little recognised in irrigation polices and is under-supported by the government. This paper explores how this situation is exacerbated by modernisation ideas in irrigation policy and professional thinking. By means of a historical review, we trace modernisation thinking in irrigation development from the colonial period onwards, and analyse how this thinking continues to play out in contemporary irrigation policies in both countries. We then examine the relationship between modernisation thinking and practices of farmer-led irrigation development, drawing on policy documents, field studies, and interviews in both countries. Based on this analysis, we argue that the nature of farmer-led development of irrigation is consistent with many of the goals identified by state agricultural modernisation programmes, but not with the means by which government and state policies envisage their achievement. As a consequence, policies and state officials tend to screen out farmers’ irrigation initiatives as not relevant to development until they are brought within state-sanctioned processes of technical design and administration.