Few-shot instance segmentation extends the few-shot learning paradigm to the instance segmentation task, which tries to segment instance objects from a query image with a few annotated examples of novel categories. Conventional approaches have attempted to address the task via prototype learning, known as point estimation. However, this mechanism is susceptible to noise and suffers from bias due to a significant scarcity of data. To overcome the disadvantages of the point estimation mechanism, we propose a novel approach, dubbed MaskDiff, which models the underlying conditional distribution of a binary mask, which is conditioned on an object region and $K$-shot information. Inspired by augmentation approaches that perturb data with Gaussian noise for populating low data density regions, we model the mask distribution with a diffusion probabilistic model. In addition, we propose to utilize classifier-free guided mask sampling to integrate category information into the binary mask generation process. Without bells and whistles, our proposed method consistently outperforms state-of-the-art methods on both base and novel classes of the COCO dataset while simultaneously being more stable than existing methods.