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The trend of implementing the IPv6 into wireless sensor networks (WSNs) has recently occurred as a consequence of a tendency of their integration with other types of IP-based networks. The paper deals with the security aspects of these IPv6-based WSNs. A brief analysis of security threats and attacks which are present in the IPv6-based WSN is given. The solution to an adaptive distributed system for malicious node detection in the IPv6-based WSN is proposed. The proposed intrusion detection system is based on distributed algorithms and a collective decision-making process. It introduces an innovative concept of probability estimation for malicious behaviour of sensor nodes. The proposed system is implemented and tested through several different scenarios in three different network topologies. Finally, the performed analysis showed that the proposed system is energy efficient and has a good capability to detect malicious nodes.