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No one has used an atom bomb on Pearl Harbor. The Japanese attacked using conventional bombs and torpedoes from carrier launched aircraft. There were also mini-subs that attempted to enter the harbor.
Japan attacked Pearl Harbor with six carriers and over 350 aircraft. Midget subs were also employed but there is no record of the exact number.ref:Hakim, Joy (1995). A History of Us: War, Peace and all that Jazz. New York: Oxford University Press.
The midget subs the Japanese launced to attack Pearl Harbor sank no ships and of their crews there was only one survivor and he was captured.
Nova - 1974 Killer Subs in Pearl Harbor 37-9 was released on: USA: 5 January 2010
Subs, Fuel depots, and repair facilities.
IJN & USN subs went looking for ships to sink.
The midget subs did no actual damage
A few aircraft and flyers and one or two mini-subs and crew.
Yes. There were a total of 5 2-man subs used at Pearl Harbor. The most recently found one was the fifth.
Approximately: 6 Fleet Carriers, 2 Battleships, 3 Cruisers, 9 Destroyers, 23 Fleet Submarines, 5 Mini-Subs (Midget Submarines), and over 400 airplanes.
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There have been reports that Japan launched several mini-subs toward Pearl Harbor.In fact, one was sunk just before the air attack began. But to answer your question, the attack on Pearl Harbor was mainly by air.