From: Romulus, MI
Given their size, range, speed, and torpedoes, Japanese submarines achieved surprisingly little. This was because they were mainly employed against warships, which were fast, maneuverable, and well-defended when compared to merchant ships. Japanese naval doctrine was built around the concept of fighting a single decisive battle, as they had done at Tsushima 40 years earlier. They thought of their submarines as scouts, whose main role was to locate, shadow, and attack Allied naval task forces.
The Japanese did, of course, make some attacks on merchant shipping in the Pacific and Indian Oceans, but these were the minority of missions. Frequently, they waited for fleets that were never seen, supported spectacularly brave but inconsequential reconnaissance flights, or toted midget submarines about, all of which achieved rather less than was possible with so valuable a resource as the Japanese submarine fleet. Worse from a naval perspective, Japanese submarines were increasingly employed in running supplies to the starving garrisons of isolated islands. The Japanese expended hundreds of sorties in this way, which might have otherwise been used offensively against the Allied war effort. A submarine's cargo capacity was much less than that of a relatively inexpensive freighter. However, Japan was understandably reluctant to let island garrisons starve. Additionally, many practically unarmed submarines (including 26 built for Army use) were built specifically for the supply role, consuming production resources as well.
Japanese doctrine and equipment
For the Imperial Japanese Navy, however, submarines, as part of the Japanese warrior tradition of bushido, preferred to attack warships rather than transports. Faced with a convoy, an Allied submarine would try to sink the merchant vessels, while their Japanese counterparts would give first priority to the escorts. This was important in 1942, before Allied warship production came up to capacity. So, while the U.S. had an unusually long supply line between its west coast and frontline areas that was vulnerable to submarine attack, Japan's submarines were instead used for long range reconnaissance and to resupply strongholds which had been cut off, such as Truk and Rabaul.
Japanese submarines accounted for about 184 merchant ships with a tonnage of 907,000 tons, ( included in these figures are 98 US ships of 520,000 tons ). In addition they sank 2 Aircraft Carriers, 2 Cruisers, and 10 Destroyers.
Over a seven-day period, from December 18 to 24, 1941, nine Japanese submarines positioned at strategic points along the U.S. west coast attacked eight American merchant ships, of which two were sunk and two damaged. Six seamen were killed. It was the first and only time during the three years and eight months of war to come that more than one Japanese submarine appeared at the same time off the American coast.
I can't find the link (didn't think to copy it down along with the above) but there was one that mentioned Japanese submarines were only allocated one torpedo per merchant ship.
PO2 US Navy (1980-1986);
USS Midway CV-41 (1981-1984)
Whidbey Island, WA (1984-1986)
Naval Reserve (1986-1992)