Innovation contexts and associated elements determine the type of innovation and adoption. This study aimed at the understanding of the innovation policy and intervention mechanism within the Bhutanese Department of Agriculture (DoA). We developed a conceptual model from the themes and the OECD evaluation criteria based on the conceptual model. The national issues and opportunities related to the agriculture and forestry of Bhutan were defined, and policy gaps were identified between the national plan and the institutional programs that were implemented. A total of 67 government documents from the relevant agencies were collected, of which, 33 documents were included, based on the inclusion criteria that matched with the conceptual, thematic analytical model. Our results from the document analysis show that the institutional innovative interventions appeared relevant to the Bhutanese context; however, inadequate coherence (mapping and alignment) of the institutional intervention programs with the national issues and goals suggested the need for the Bhutanese agricultural innovation system to enhance the effectiveness and efficiency of the program results. Similarly, coordination and collaboration were found to be necessary to extract the synergistic impact of the innovative interventions at the various levels of administrative hierarchy. Institutional accountability and interventional coherence at different organisational levels needs reviewing in order to achieve the sustainability of the outcome in Bhutanese agricultural research.