Latest intelligent vehicles require a higher level of reliability for controller area network (CAN). Furthermore, the spread of electric vehicles may worsen the problem of electromagnetic interference. Severe electromagnetic interference can affect the bit error rate of the frames being communicated, leading to more frequent inconsistent message omission (IMO) or inconsistent message duplication (IMD) faults, which can be attributed to defects in the retransmission mechanism of CAN. To address the problems of IMO and IMD, this paper presents a dual-channel network structure and corresponding operating protocol, named as fault-tolerant dual-channel CAN. The IMO occurrence rate is maintained at a considerably low level by employing a dual-channel CAN over which replicate messages are transmitted. At the same time, any duplicate frames caused by IMD are identified and removed by analyzing the frame reception time. The integrity of the proposed network structure and operating protocol are evaluated through formal verification.