For monitoring the night sky conditions, wide-angle all-sky cameras are used in most astronomical observatories to monitor the sky cloudiness. In this manuscript, we apply a deep-learning approach for automating the identification of precipitation clouds in all-sky camera data as a cloud warning system. We construct our original training and test sets using the all-sky camera image archive of the Iranian National Observatory (INO). The training and test set images are labeled manually based on their potential rainfall and their distribution in the sky. We train our model on a set of roughly 2445 images taken by the INO all-sky camera through the deep learning method based on the EfficientNet network. Our model reaches an average accuracy of 99\% in determining the cloud rainfall's potential and an accuracy of 96\% for cloud coverage. To enable a comprehensive comparison and evaluate the performance of alternative architectures for the task, we additionally trained three models LeNet, DeiT, and AlexNet. This approach can be used for early warning of incoming dangerous clouds toward telescopes and harnesses the power of deep learning to automatically analyze vast amounts of all-sky camera data and accurately identify precipitation clouds formations. Our trained model can be deployed for real-time analysis, enabling the rapid identification of potential threats, and offering a scaleable solution that can improve our ability to safeguard telescopes and instruments in observatories. This is important now that numerous small and medium-sized telescopes are increasingly integrated with smart control systems to reduce manual operation.