The relevance of the study is conditioned by the need to revise the methods of farming with a focus on the use of innovative technologies to improve the quality and quantity of output. The purpose of the study is to analyse the problems and prospects of agricultural production in the Republic of Kazakhstan to create a comprehensive innovative model for the further development of the agro-industrial sector. The study of the prospects for the modernised improvement of the agro-industrial complex of the Republic of Kazakhstan was carried out in three stages based on the functional and logical, systemic, and structural approaches using methods of analysis, synthesis, comparison, systematisation, SWOT analysis, and statistical data processing. The analysis of research papers of Kazakhstani and foreign researchers was carried out to separate the problems and opportunities of agriculture of the Republic of Kazakhstan. It is determined that the agricultural complex of the state is represented by three forms of management, including farming, cooperatives, and the main business. The features of innovative activity and types of innovations in agriculture are considered. The possibilities and strengths of agriculture of the Republic of Kazakhstan are substantiated in accordance with the statistical data of gross output for 2012-2019. The organisational model of further development of the agro-industrial complex of the state in the context of the application of innovative technologies and the establishment of relationships with state information systems is proposed. The practical value of the study consists in providing a general analysis of both the problems and prospects of agriculture in the Republic of Kazakhstan, as a result of which a comprehensive model of innovative development was compiled