The author’s approach to a problem of management by innovative risks in agrarian and industrial complex is developed. Classification of risks of innovative projects in agrarian and industrial complex is presented, actions for risk management at stages of development and implementation of the innovative project Are offered. The directions of formation of a control system by risks of innovative projects in agrarian and industrial complex depending on stages risk – the management, representing algorithm of consecutive actions from risk identification before control of efficiency of carried-out actions are developed.