A strategic issue in national development is the integration between national and regional planning. This research had the aims to: (1) analyse the consistency and integration between national and regional plans, (2) analyse the consistency of national and regional planning with the actual implementation, and (3) analyse the factors that influenced the inconsistencies of national and regional planning in the agricultural sectors. The research was carried out by the Ministry of Agriculture (MoA), Indramayu Regency, in West Java Province and South Lampung Regency in Lampung Province. The data were analysed using both content and consistency analyses and a comparative case study. The research results showed that: (1) the level of consistency between the planning documents from the MoA and those from Indramayu Regency reached 87.68% and 95.81%, when compared with those from South Lampung Regency; (2) in terms of the consistency between the documents and the actual implementation, South Lampung Regency had programs/activities which were more integrated with the MoA programs compared with Indramayu Regency; and (3) there were five main factors which caused inconsistencies: policies from the district heads and the parties involved, force majeure, the development priorities, the communication distortion, and support from the political parties. The central government (the MoA) and the Regional Agriculture Office must collaborate by making an electronic-based priority scale of development planning and by reinforcing the capacities of regional planners.