The energy system is a complex socio-technical system, characterised by a multitude of stakeholders, different goals, long-term investments, and large scale sub systems with long lifetimes. The government of the Netherlands aims to support the transition of the energy system of the Netherlands towards a sustainable system by implementing policy measures. Recently, companies have voiced their concerns on the fluctuating effects of policy measures in the Netherlands and have asked for a more long term vision of policy measures. This long term vision can be (partly) provided by analysing the interference in the energy system. Another component of a policy strategy is that to develop and implement a long term policy strategy, multiple governmental organisation have to collaborate. The policy measures are designed by different ministries within the Netherlands. In order to implement the coherent policy strategy, collaboration between these ministries is essential. This research proposes a methodology to identify five types of interference and to analyse the effects of the identified interference on the Dutch energy system. This categorization of interference allows for a discussion on the unavoidable nature of interference. Moreover, it shows which types of interference can prove to be beneficial at certain times. A conceptual theoretical framework for factors that influence interorganizational collaboration between public parties has been constructed based on literature, and is tested and validated within the case study. The research into interorganizational collaboration also includes a focus on the relations between the identified factors. The relations can provide insight into the more complex system view of the factors that influence interorganizational collaboration between public parties. Both researches are based on a view of the world in systems, and for both is searched for links between sub-systems. Finding the link between the technical energy system and the collaborations required in policy making was based on this system perspective. These two topics are invariably linked together. The integrations in the energy system increases the need for collaboration, whereas collaboration can increase (the effectiveness of) the integrations in the energy system.