Embodiments of the disclosure provide a method for controlling a power generation system during on-line maintenance. The method includes operating the power generation system in a first maintenance mode, which causes a controller of the power generation system to disable an automated response to at least one operational fault of the power generation system; monitoring a risk parameter of the power generation system or at least one sensor within the power generation system while operating the power generation system in the first maintenance mode; and operating the power generation system in a second maintenance mode in response to detecting an override command, an elapsed time exceeding a time limit, or the monitored risk parameter exceeding a safety threshold. The second maintenance mode causes the controller of the power generation system to enable the automated response to the at least one operational fault of the power generation system.