In Wireless Sensor Networks (WSNs), detecting malicious nodes and discarding their sensed data have a significant importance to carry out the mission critical tasks. Traditional security measures such as authentication and encryption cannot be implemented directly to WSNs due to the limited resources of sensor nodes. Hence, novel energy efficient methods are needed to minimize the effect of malicious nodes. In this paper, a hybrid Intrusion Detection System (IDS) for clustered WSNs is proposed. The proposed IDS is based on functional reputation and misuse detection rules. The main idea is that each sensor node computes functional reputation values for its neighbors by observing their activities. Base Station (BS) detects malicious nodes by combining functional reputation values and misuse detection rules. According to the simulation results, the proposed approach increases the network lifetime and improves sensed data freshness by detecting malicious nodes in a centralized way without surging energy consumption.