The article deals with the issues related to the monitoring of R&D projects supported by the public funds. In accordance with the current legislation, monitoring of scientific, technical and innovation projects is carried out within the framework of the structural elements of state programs. To conduct monitoring, results, control points and objects of scientific and technical activities should be established. At the same time, however, within the framework of the three forms of financial support for the implementation of R&D projects - grant financing, subsidies for the implementation of public assignments, public procurement - different monitoring methods and procedures are applied. Further, the names of the control points are not linked to the results of projects in terms of technology readiness levels (TRL). Finally, information systems that support the monitoring and evaluation of R&D results are not fully compatible with each other. As a result, the overall effectiveness of monitoring decreases, which leads to delays in making managerial decisions and entails wasteful spending of budget funds. In the leading OECD countries, there is a practice of centralized methodological support of the implementation of R&D and innovation, which provides an unified approach to management of such projects and conjugation of state support at all stages of innovation cycle. Successful project management involves application of such specific management tools as the stage gates model and TRL methodology, which provide effective monitoring of results and flexibility in making management decisions, including the possibility of adjusting the basic parameters of projects at different stages of their implementation. The experience of foreign countries shows that in order to improve the quality and effectiveness of monitoring of R&D projects in Russia, it is necessary to ensure the harmonization of general and sectoral legislation governing the monitoring of the results of research, development and innovation projects, which will ensure the formation of a unified approach within the framework of project management of state programs. It is advisable to extend the rules for monitoring the results of R&D adopted in the system of grant financial support to the systems of public assignment and public procurement in this area of activity, creating conditions for the conjugation of various forms of public support. Finally, it is necessary to improve operation of the existing state information resources for the management of scientific, technical and innovation projects.