Throughout the war, Japan was dependent on sea transport to provide adequate resources, including food, to the home islands and supply its military at garrisons across the Pacific. Before the war, Japan estimated the nation required 5.9 million tons of shipping to maintain the domestic economy and military during a major war, which was considerably less than the 6.4 million tons of shipping in the Japanese merchant fleet and 1.2 million tons of smaller craft at the time of the attack on Pearl Harbor. Despite the awareness shipping was vital, the Japanese military accorded anti-submarine warfare a low priority and allocated few warships and aircraft to protecting merchant shipping. Moreover, Japanese Navy doctrine in relation to commerce defense was derisively bad.
The size and effectiveness of the Allied submarine force increased greatly during the Pacific War. At the start of the war, a high proportion of the submarines deployed against the Japanese were obsolete and U.S. boats were hampered by defects in their primary weapon, the Mark 14 torpedo, as well as by poor training (an excessive reliance on sonar, due to an undue fear of destroyers' sonar and aircraft), insufficiently aggressive skippers, poor dispositions (scattered on close surveillance of Japan's major bases), and divided command (which kept submarines out of one of the best hunting areas, the Luzon Strait, for fear of fratricide). Growing numbers of modern submarines became available from 1942 onwards and, assisted by signals intelligence (breaking the "maru code" in January 1943, after a gaffe by U.S. Customs prewar had caused Japan to change it), and the rectification of the Mark 14's problems (but not until September 1943), U.S. submarines inflicted devastating losses on Japanese merchant shipping in 1943 and 1944. In conjunction with attacks by aircraft, including aerial mine laying, U.S. submarines had effectively destroyed the Japanese merchant fleet by the end of the war. Poor torpedoes claimed at least three U.S. submarines and command errors at least one more, out of forty-two lost in action.
While Britain stationed a force of submarines in the Far East prior to the outbreak of war, none were available in December 1941. The British had 15 modern submarines in the Far East in September 1939. These submarines formed part of the China Station and were organised into the 4th Flotilla. Although the number of British submarines in the Far East increased in early 1940 when the 8th Flotilla arrived at Ceylon, both flotillas and all their submarines were withdrawn in mid-1940 to reinforce the Mediterranean Fleet.
The Netherlands also maintained a submarine force in the Far East in order to protect the Netherlands East Indies (NEI). In December 1941 this force comprised 15 boats based at Surabaya, most of which were obsolete.
In a break with pre-war doctrine (which, like Japan's, had presumed a rush across the Pacific and a "decisive battle" between battleships) and the London Naval Treaty, U.S. naval commanders in the Pacific were ordered to "execute unrestricted air and submarine warfare against Japan" on the afternoon of 7 December 1941. The Pacific Fleet Submarine Force had emerged unscathed from the attack on Pearl Harbor and USS Gudgeon departed on the fleet's first offensive war patrol on 11 December 1941. The Asiatic Fleet's 27 submarines (including more fleet boats than at Pearl Harbor) also went into action on 7 December and began war patrols in the waters around the Philippines and Indochina. Thanks to inadequate prewar planning, which made no provision for defensive minelaying, nor placing submarines on station around the Philippines nor off enemy harbors, the Asiatic Fleet's efforts to counter the Japanese invasion of the Philippines were unsuccessful and the Fleet's surviving submarines were forced to withdraw to Surabaya in the NEI.
British, Dutch, and US submarines took part in the unsuccessful defence of Malaya and the NEI in late 1941 and early 1942. In December 1941, five Dutch submarines attacked the Japanese invasion fleet off Malaya. These submarines sank two Japanese merchant ships and damaged four others, but three of the attackers were sunk. The two surviving Dutch submarines were withdrawn to defend the NEI where they were assisted by two British submarines, which had been transferred from the Mediterranean Fleet, and several US boats. The US Asiatic Fleet's submarine force left Surabaya for Fremantle in Australia on 1 March. (They would remain in Australia, on the most hazardous stations for U.S. submarines, for the duration.) By this date the Asiatic Fleet's 27 submarines had sunk only 12 Japanese ships for the loss of four US boats. Following the fall of the NEI, only a handful of British and Dutch submarines were based in the Indian Ocean, and these had little impact on Japanese forces in the area.
The British submarine force expanded its areas of operation in the last months of the war. In late 1944 the Eighth Flotilla, with 11 British and Dutch submarines, was transferred to Fremantle and operated in the Java Sea and surrounding areas under the command of the US Seventh Fleet. The Fourth Flotilla and the newly-formed Second Flotilla remained at Ceylon. By March 1945 the British boats had gained control of the Strait of Malacca, preventing any supplies from reaching the Japanese forces in Burma by sea. By this time there were few large Japanese ships in the region, and the submarines mainly operated against small ships which they attacked with their deck guns. In April the Eighth Flotilla moved to Subic Bay in the Philippines and the Fourth Flotilla replaced it at Fremantle. At this time there were 38 British and Dutch submarines in the theatre, and an additional five boats on their way from Europe. Three British submarines (HMS Stonehenge, Stratagem and Porpoise) were sunk by the Japanese during the war.
As figures for the size of the Japanese merchant marine and its losses differ between different sources it is not possible to provide a definitive accounting of the state of the merchant marine over the course of the war. The following tables show different assessments of Japanese losses and construction.
Size of the Japanese merchant fleet during World War II (all figures in tons)
| Date | Additions | Losses | Net change | End of period total | Index |
| 12/07/1941 | 6,384,000 | 100 | |||
| 12/1941 | 44,200 | 51,600 | -7,400 | 6,376,600 | 99 |
| 1942 | 661,800 | 1,095,800 | -434,000 | 5,942,600 | 93 |
| 1943 | 1,067,100 | 2,065,700 | -998,600 | 4,494,400 | 77 |
| 1944 | 1,735,100 | 4,115,100 | -2,380,000 | 2,564,000 | 40 |
| 1/45 - 8/45 | 465,000 | 1,562,100 | -1,097,100 | 1,466,900 | 23 |
Japanese merchant fleet losses during World War II (all figures in tons, taken from JANAC)
| Date | Starting tonnage | Additions | Losses | Net change | End of period total |
| 1942 (including 12/41) | 5,975,000 | 111,000 | 725,000 | -89,000 | 5,886,000 |
| 1943 | 5,886,000 | 177,000 | 1,500,000 | -1,323,000 | 4,963,000 |
| 1944 | 4,963,000 | 624,000 | 2,700,000 | -2,076,000 | 2,887,000 |
| 1945 | 2,887,000 | ? | 415,000 | -415,000 | 2,472,000 |
| end of war | -3,903,000 | 1,983,000 | |||
Britain also deployed a flotilla of midget submarines to the Far East which were used to conduct sabotage raids. The Fourteenth Flotilla, which was equipped with six XE class submarines, arrived in Australia in April 1945 but was almost disbanded in May as no suitable targets could be found. The Flotilla's fortunes improved in early June, however, when undersea telegraph lines in the South China Sea were identified as being worthwhile targets along with a heavy cruiser at Singapore. On 31 July XE4 cut the submerged Singapore-Saigon telegraph cable near Cape St. Jacques in French Indochina and XE5 cut the Hong Kong-Saigon cable close to Lamma Island, Hong Kong. At the same time XE1 and XE3 penetrated the Straits of Johor where they severely damaged the Japanese heavy cruiser Takao with limpet mines.