A method and apparatus of controlling an engine at the time of first combustion during start-up in which an increase in an engine speed can be regulated, and thus noises and vibrations of the engine are reduced, and a personal watercraft which does not unintentionally start moving at start-up. The method comprising the steps of detecting the start-up of the engine; detecting a warm-up condition of the engine; and controlling the engine to inhibit combustion of at least one of the cylinders of the engine according to the warm-up condition upon the detection of the start-up.