Actually, it was caused by their equivalent of a Mark 48 heavyweight torpedo.
Imagine now building a submarine that would launch cavitating torpedo/missiles that would cruise under the water at high speeds until just offshore, at which point they come up out of the water and act like a cruise missile, flying at less than 500 feet and impacting a city before anyone even knew they were coming.
The weapon would be bigger than most submarines, or the underwater phase would be extremely short.