A boat propulsion unit controller includes a switch arranged to switch between a long intake duct and a short intake duct for drawing air into an engine of a boat propulsion unit, a motor-operated driver arranged to drive the switch, a duct length switching position sensor arranged to detect the position of the switch at the time of switching the duct length, a fuel supply arranged to supply fuel to the engine, a sensor failure detector arranged to detect failure of the duct length switching position sensor based on its output, and a controller arranged to compensate the fuel supply rate based on the position of the switch detected at the time of duct length switchover. A controller, when the duct length switching position sensor fails, takes the action of switching to the long intake duct and compensates the fuel supply rate using a sensor output quasi value corresponding to the time of switchover to the long intake duct. Engine performance may be maintained as much as possible even when duct length switchover fails due to frequent duct length switchover actions.