Secure and privacy-preserving health status representation learning has become a critical challenge in clinical prediction systems. While deep learning models require substantial high-quality data for training, electronic health records are often restricted by strict privacy regulations and institutional policies, particularly during emerging health crises. Traditional approaches to data integration across medical institutions face significant privacy and security challenges, as healthcare providers cannot directly share patient data. This work presents MultiProg, a secure federated learning framework for clinical representation learning. Our approach enables multiple medical institutions to collaborate without exchanging raw patient data, maintaining data locality while improving model performance. The framework employs a multi-channel architecture where institutions share only the low-level feature extraction layers, protecting sensitive patient information. We introduce a feature calibration mechanism that ensures robust performance even with heterogeneous feature sets across different institutions. Through extensive experiments, we demonstrate that the framework successfully enables secure knowledge sharing across institutions without compromising sensitive patient data, achieving enhanced predictive capabilities compared to isolated institutional models. Compared to state-of-the-art methods, our approach achieves the best performance across multiple datasets with statistically significant improvements.