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In this paper, we introduce ProtoOcc, a novel 3D occupancy prediction model designed to predict the occupancy states and semantic classes of 3D voxels through a deep semantic understanding of scenes. ProtoOcc consists of two main components: the Dual Branch Encoder (DBE) and the Prototype Query Decoder (PQD). The DBE produces a new 3D voxel representation by combining 3D voxel and BEV representations across multiple scales through a dual branch structure. This design enhances both performance and computational efficiency by providing a large receptive field for the BEV representation while maintaining a smaller receptive field for the voxel representation. The PQD introduces Prototype Queries to accelerate the decoding process. Scene-Adaptive Prototypes are derived from the 3D voxel features of input sample, while Scene-Agnostic Prototypes are computed by applying Scene-Adaptive Prototypes to an Exponential Moving Average during the training phase. By using these prototype-based queries for decoding, we can directly predict 3D occupancy in a single step, eliminating the need for iterative Transformer decoding. Additionally, we propose the Robust Prototype Learning, which injects noise into prototype generation process and trains the model to denoise during the training phase. ProtoOcc achieves state-of-the-art performance with 45.02% mIoU on the Occ3D-nuScenes benchmark. For single-frame method, it reaches 39.56% mIoU with an inference speed of 12.83 FPS on an NVIDIA RTX 3090. Our code can be found at https://github.com/SPA-junghokim/ProtoOcc.