In this paper, the authors present a modified version of the Partition Ciphering System (PCS) encryption system previously proposed. The previously developed encryption system PCS uses the partition problem to encrypt a message. The goals of newly developed system are avoiding statistical and frequency attacks, by providing a balance between 0s and 1s, ensuring a good level of entropy and achieving confidentiality through encryption. One of the novelties of the new design compared to its predecessor is the use of cellular automata (CAs) during the encryption. The use of CAs is justified by their good cryptographic properties that provide a level of security against attacks, and better confusion and diffusion properties. The new design is first presented with details of the encryption and decryption mechanisms. Then, the results of the DIEHARDER battery of tests, the results of the avalanche test, a security analysis and the performance of the system are outlined. Finally, a comparison between CA-PCS and PCS as well as the AES encryption system is provided. The paper shows that the modified version of PCS displays a better performance as well as a good level of security against attacks.