Current transformers (CTs) are one of the key constituents of power system instrumentation and measurement, and their failure may lead to a breakdown of the entire protection scheme. The CT replacement or repair may not be feasible every time a CT malfunctions at a remote distribution substation as rural areas generally lack adequate skilled manpower. This paper presents a multi-agent system based substation automation solution to improve the reliability of protection system during any CT failure. It employs a special function protection scheme for making quick replacements of faulted CTs associated with current differential relay (87). The proposed autonomous protection scheme has been tested on a typical American Electric Power (AEP) distribution substation using MATLAB/Simulink and Java Agent DEvelopment Framework (JADE).