In this paper an approach based on system identification is used for fault detection in a nuclear reactor. A continuous-time Extended Kalman Filter (EKF) is presented, which allows the parameters of the nonlinear system to be estimated. Also a fault tolerant control system is designed for the nuclear reactor during power changes operation. The proposed controller is an adaptive critic-based neuro-fuzzy controller. Performance of the controller in terms of transient response and robustness against failures is very good and considerable. (C) 2014 Elsevier Ltd. All rights reserved.