The present invention relates to an engine protecting apparatus for preventing the inflow of moisture, which drops the RPM (revolutions per minute) of an engine by generating an RPM drop request signal when moisture drain does not occur, wherein a time is counted from the point when a moisture detection signal is received from a WIF sensor installed in a moisture separator, and moisture drain is checked at the point when a counted cumulative time exceeds a set time. When moisture drain is not performed even after a signal for moisture drain is received from a moisture detecting sensor installed in the moisture separator, a driver is aware of the seriousness of moisture separation to thus separate moisture in the moisture separator as soon as possible. This prevents fatal damages which may be aroused in an injector or fuel system due to the introduction of moisture into an engine.