CAN is widely used as an in-vehicle network. However, since security of CAN protocol is not enough, various attacks on in-vehicle system have been reported. Therefore, as a countermeasure against the attacks, message authentication using a Message Authentication Code (MAC) has been proposed. In message authentication that also prevents replay attack, a counter is used for MAC generation. However, if the counters are out of synchronization between sender and receiver, subsequent messages cannot be authenticated. Therefore, a counter synchronization function is required to continue communication using message authentication. This study proposes a new counter synchronization method for message authentication in CAN communication. The proposed method synchronizes the counters using resynchronization message, which is based on a newly introduced synchronization counter. In order to reduce the communication traffic, the proposed method sends only the difference between the introduced counter and the counter for MAC generation. Experiments using mock-up system prove the validity of the proposed method.