Cooperative autonomous systems (CAS) are explored in multiple fields of industrial IoT systems (IIoT) to solve complex tasks, sharing information and task execution. CAS have different objectives and are usually controlled by different administrators. Cooperation also comes with security and privacy challenges. Architectures have been proposed for limited use-cases or for specific security and performance issues. We argue that a unified reference architecture for CAS is needed for security, efficiency and customization. We propose such an architecture called RACAS to design efficient and modular CAS and show how it can be secured on-demand. We illustrate how RACAS can be applied to an intelligent transportation system including networks of autonomous and connected vehicles.