<p>We present a statistical framework based on the gravity model to analyze inter-organizational research collaboration to assess the fragmentation of a national research system. We focus on the Dutch research system during the period 2010–2022 characterized by multiple policy changes to reduce the fragmentation and to align agendas among the key organizations: classic universities, technical universities, university medical centers, universities of applied sciences, and public research organizations. Using the gravity equation, we explain the intensity of collaboration between any two organizations while controlling for their respective sizes and travel distance. By looking at the standardized residuals of the regression analysis over time, we assess whether organizations tend to collaborate more or less than what can be expected from their respective sizes and travel distance. Our main finding holds that a process of defragmentation of the Dutch research system is somewhat visible, especially in closer collaborations between the universities of applied sciences (UAS) with other organizations. At the same time, technical and classic universities have become more detached from each other. And, public research organizations have not become much more integrated within the research system, despite calls to do so. These findings suggest that the process of integration is a variegated and slow one, exposing the limited ability of national governments to steer research systems in top-down manners.</p>