A two-level hierarchical management system for the innovation implementation in organizations is studied. There are several lower-level management subjects (agents) and one top-level management subject (supervisor) in it. It is assumed that all subjects tend to maximize their gains. The supervisor manages the innovation implementation using different information regulations. Algorithms for constructing the Stackelberg equilibria with and without management feedback under motivation and compulsion are presented. The Stackelberg equilibria were constructed using the method of qualitatively representative scenarios (QRS). Numerical experiments were conducted, the results analyzed, and recommendations made for the implementation of innovative technologies in organizations.