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This paper introduces a novel LiDAR point cloud data encoding solution that is compact, flexible, and fully supports distributed data storage within the Hadoop distributed computing environment. The proposed data encoding solution is developed based on Sequence File and Google Protocol Buffers. Sequence File is a generic splittable binary file format built in the Hadoop framework for storage of arbitrary binary data. The key challenge in adopting the Sequence File format for LiDAR data is in the strategy for effectively encoding the LiDAR data as binary sequences in a way that the data can be represented compactly, while allowing necessary mutation. For that purpose, a data encoding solution, based on Google Protocol Buffers (a language-neutral, cross-platform, extensible data serialisation framework) was developed and evaluated. Since neither of the underlying technologies is sufficient to completely and efficiently represent all necessary point formats for distributed computing, an innovative fusion of them was required to provide a viable data storage solution. This paper presents the details of such a data encoding implementation and rigorously evaluates the efficiency of the proposed data encoding solution. Benchmarking was done against a straightforward, naive text encoding implementation using a high-density aerial LiDAR scan of a portion of Dublin, Ireland. The results demonstrated a 6-times reduction in data volume, a 4-times reduction in database ingestion time, and up to a 5 times reduction in querying time.