This thesis is concerned with the organisation of innovation in the interaction between multinational companies and host-country innovation systems. It proposes a framework for characterising the decentralised governance of innovation projects in sectors and identifying emerging organisational configurations in this specific context. The general characteristics of the project-based knowledge networks are examined in terms of (i) the shifting boundaries between subsidiaries and technological partners, (ii) the specialisation of actors in types of activities and (iii) the speed of change in the collaborations between multinational companies and technological institutes. The emerging configurations are classified in terms of (i) the knowledge and resources flows in different innovation projects and (ii) the common aims of the different groups of stakeholders. This framework is applied on the decentralised networks of innovation projects in the Brazilian ICT sector promoted by tax incentives to innovation activities (―Brazilian ICT Law‖). The empirical analysis combines the data of more than 10,000 innovation projects and in-depth case studies on the organisation of innovative activities in 11 R&D laboratories in subsidiaries of multinational companies and 11 of their main technological partners. The analysis of the project-based knowledge networks and emerging configurations is recognised as a useful tool for examining the dynamics promoted by the sectoral policy. This research provides insights on how the institutional framework such as the Brazilian ICT Law provided the space for the decentralised interaction between different organisations with very different interests. The analysis also shows that the regulation may support higher investments in R&D, but it does not necessarily enforce a project portfolio that promotes a sustainable knowledge flow between multinational companies and the sectoral innovation system. Finally, the thesis includes specific recommendations for addressing key challenges such as the organisational development of the subsidiaries, the emergence of private research institutes and the coordination of sectoral policies. Keywords: sectoral innovation systems, knowledge network, organisation of innovation, economic sociology, R&D policy, innovation projects, project-based learning, interorganisational networks