The current sanitary emergency situation caused by COVID-19 has increased the interest in controlling the flow of people in indoor infrastructures, to ensure compliance with the established security measures. Top view camera-based solutions have proven to be an effective and non-invasive approach to accomplish this task. Nevertheless, current solutions suffer from scalability problems: they cover limited range areas to avoid dealing with occlusions and only work with single camera scenarios. To overcome these problems, we present an efficient and scalable people flow monitoring system that relies on three main pillars: an optimized top view human detection neural network based on YOLO-V4, capable of working with data from cameras at different heights; a multi-camera 3D detection projection and fusion procedure, which uses the camera calibration parameters for an accurate real-world positioning; and a tracking algorithm which jointly processes the 3D detections coming from all the cameras, allowing the traceability of individuals across the entire infrastructure. The conducted experiments show that the proposed system generates robust performance indicators and that it is suitable for real-time applications to control sanitary measures in large infrastructures. Furthermore, the proposed projection approach achieves an average positioning error below 0.2 meters, with an improvement of more than 4 times compared to other methods.