In this paper, we propose a novel use of network intrusion detection systems (NIDSs) tailored to detect attacks against networks that support hybrid controllers that implement power grid protection schemes. In our approach, we implement specification-based intrusion detection signatures based on the execution of the hybrid automata that specify the communication rules and physical limits that the system should obey. To validate our idea, we developed an experimental framework consisting of a simulation of the physical system and an emulation of the master controller, which serves as the digital relay that implements the protection mechanism. Our Hybrid Control NIDS (HC-NIDS) continuously monitors and analyzes the network traffic exchanged within the physical system. It identifies traffic that deviates from the expected communication pattern or physical limitations, which could place the system in an unsafe mode of operation. Our experimental analysis demonstrates that our approach is able to detect a diverse range of attack scenarios aimed at compromising the physical process by leveraging information about the physical part of the power system.