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To reach human performance on complex tasks, a key ability for artificial systems is to understand physical interactions between objects, and predict future outcomes of a situation. This ability, often referred to as intuitive physics, has recently received attention and several methods were proposed to learn these physical rules from video sequences. Yet, most of these methods are restricted to the case where no, or only limited, occlusions occur. In this work we propose a probabilistic formulation of learning intuitive physics in 3D scenes with significant inter-object occlusions. In our formulation, object positions are modeled as latent variables enabling the reconstruction of the scene. We then propose a series of approximations that make this problem tractable. Object proposals are linked across frames using a combination of a recurrent interaction network, modeling the physics in object space, and a compositional renderer, modeling the way in which objects project onto pixel space. We demonstrate significant improvements over state-of-the-art in the intuitive physics benchmark of IntPhys. We apply our method to a second dataset with increasing levels of occlusions, showing it realistically predicts segmentation masks up to 30 frames in the future. Finally, we also show results on predicting motion of objects in real videos.