When developing a Wi-Fi indoor positioning system in a real-world environment, the problems we have to face are that some access points’ signal strength fluctuates extensively or even loses contact due to the cybersecurity threats, leading to the fact that the indoor location system cannot get reliable application in a real-world environment. To solve this problem, we propose a new integrated model based on signal anomaly detector and signal distance corrector to provide reliable position estimation when the access points’ signal is lost under cybersecurity threats. The signal anomaly detector improves recognition capability of the uncertain signal and noise, while the signal distance corrector improves the robustness and fault tolerance of the highly variable Wi-Fi signals. To fully reflect the performance of the proposed method, experiments have been carried out in the real environment of indoor parking lots. The results show that the proposed integrated model successfully provides reliable position estimation when the access points are lost under cybersecurity threats.