This has been touched on a bit in two previous posts, but I'll elaborate on it here: Japan's merchant fleet was inadequate and what she had was improperly used.
This came down to four points:
(1) japan entered the war with too few merchant ships (including those operated by the IJN and IJA)
(2) She inadequately protected the ships she did have (rarely sailing them in convoys or with sufficient escort vessels)
(3) Japan didn't use her ships efficiently. For example, a ship operated by the Army might take a cargo from Japan to Java but return with an empty hold, but a navy ship might sail to Java with an empty hold and return with a full load (this also related to the incredible degree of non-cooperation between the IJA and IJN)
(4) Japan didn't have the resources to fully replace it's merchant shipping losses during the war.
As a result, the Japanese never was able to ship as much men, material and oil and they should have and the situation rapidly declined by the end of the war.
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