The article offers an analysis of the digital technologies influence on the national innovation system transformation and related changes in goals and government innovation policy. The author elaborates the idea that the leading global companies of digital economy based their technological and market power on intensive research and development activity. Prolonged investment in new knowledge, new technologies and global innovation make IT companies the leaders and dominant segment of innovation systems. It is constantly growing, rising their own material and financial resources turning independent from the government. Moreover, they have their own technology policy being sometimes in contradiction with the governments of different levels. National as well as foreign. The problem is especially strong because the leading IT companies acting as monopolists on the foreign markets. The technology protection policy and other new form of new digital regulation are going globally.