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This paper focuses on a coding approach for effective analysis and design of secure watermark-based multimedia authentication systems. We provide a design framework for semi-fragile watermark-based authentication such that both objectives of robustness and fragility are effectively controlled and achieved. Robustness and fragility are characterized as two types of authentication errors. The authentication embedding and verification structures of the semi-fragile schemes are derived and implemented using lattice codes to minimize these errors. Based on the specific security requirements of authentication, cryptographic techniques are incorporated to design a secure authentication code structure. Using nested lattice codes, a new approach, called MSB-LSB decomposition, is proposed which we show to be more secure than previous methods. Tradeoffs between authentication distortion and implementation efficiency of the secure authentication code are also investigated. Simulations of semi-fragile authentication methods on real images demonstrate the effectiveness of the MSB-LSB approach in simultaneously achieving security, robustness, and fragility objectives.