Computerized control systems play a vital role in modern critical infrastructure. These systems are designed to provide better functionality and performance without concerning of security. This leaves them extremely vulnerable to cyber attacks which may lead to serious consequences. Therefore, it is of utmost importance to analyze the vulnerabilities of such system to protect them against various threats. In this thesis, several vulnerabilities of the open source automation system Beremiz were analyzed while considering several attack vectors that may affect the control system. To resolve some of the existing flaws, a secure communication protocol and an authentication system was implemented. The total development process was done using Acceptance Test Driven Development method and was tested with an automated testing framework "Twister".