It's pretty simple, really. Power = energy / time.
To go into a little more detail, when a laser is pulsed instead of being continuous, the desired result is to compress the amount of energy being released. So, although the amount of work being done is technically the same, the amount of energy can be orders of magnitude different. I suppose the best way to think about it is like with momentum; you might think the amount of mass the typical bullet has is pitiful -- typically only weighing a few grams -- but when shot at the speeds they are, they can do a lot of damage. By comparison, if a 1kg bowling ball were to exert the exact same amount of work that a typical bullet does, it would only end up moving at a jogging pace.