This paper proposes a novel methodology for fault section estimation in electrical power systems based on binary integer programming (BIP). The operators of control centers are sometimes overloaded by the number of alarm messages produced when protection operate to clear faults. The main motivation for this work is the development of an alarm processing tool to support the operator decisions after disturbances in order to enhance the service reliability and reduce the power restoration time. The BIP model classifies SCADA alarms to estimate the faulted section and also to identify the malfunctioned protective devices. Possible fault scenarios were considered in part of a real Brazilian power system to validate the methodology. The results show that the proposed approach can find the optimal solution even in case of multiple faults or in case of protection devices failures.