Cyber-Manufacturing System (CMS) is an innovative factory of the future, where manufacturing information is being constantly exchanged among many entities through various computer networks including the Internet. However, CMS ushers in the unique security challenges from the sheer volume and pervasiveness of exchanged data, and increased accessibility of the system by its outsiders and insiders. Also, the connections among the physical components can reveal accessible routes into the system. This research presents a unique approach to secure CMS augmented by a Blockchain. The secure Cyber-Manufacturing System with Blockchain consists of four layers: User layer, Provider layer, Service layer, and Blockchain layer. To validate how the system enables safe communications in CMS, auditing physical data through the private blockchain was experimented on a CMS testbed. The results of three different physical data audits are compared; the system’s effectiveness is demonstrated.