What were the differences between the occupation of Japan and Germany that allowed this to happen?
From an earlier answer of mine
Although the US presence looms large in Supreme Commander for the Allied Powers (SCAP)'s occupation of Japan, the occupation of the home islands was not a US-only affair. There was a British Commonwealth Occupation Force (BCOF), dominated largely by Australians that operated under GHQ's authority. The BCOF included contingents drawn from the British Empire and the Commonwealth with headquarters in Kure. But the BCOF was largely a failure; it was an expensive undertaking without any true mission for it. Still, the BCOF was not an analogue to the division of Germany. This was by design as the US took active measures to ensure that US authority would prevail over the home islands.
The decision to transform the occupation of Japan into an American-run show was not exactly straightforward. The Pentagon initially envisioned a division of the Japanese archipelago into multiple occupation zones. The Joint War Plans Committee produced one plan, JWPC-385/1, entitled "Ultimate Occupation of Japan and Japanese Territories," on 16 August 1945. JWPC-385/1 envisioned splitting the home islands between the US, the Soviets, UK/Commonwealth, and China with Tokyo split between the four powers. The USSR would receive northern Honshu and Hokkaido, while the Americans governed Honshu, the RoC and US held the Kansai region with Chinese control over Shikoku, and the UK governing southern Honshu and Kyushu. As with the occupation of Germany, this occupation mixed geographic logic- the Soviets in the north, for example- with a somewhat haphazard and arbitrary division lines. JWPC-385/1 planned for a staged occupation with a degree of collective leadership that would terminate within a few years with a final peace treaty between a reformed Japanese government and the Allied powers.
JWPC-385/1 though was a dead letter as the Pentagon was drawing it up. Both the State Department and President Truman did not want to replicate Germany in the Far East. Truman would later recall in his memoirs:
I was determined that the Japanese occupation should not follow in the footsteps of the German experience. I did not want divided control or separate zones. I did not want to give the Russians any opportunity to behave as they had in Germany and Austria.
Although Truman's claim has to be seen within the context of the early Cold War and an ex post facto justification of his actions, he was moving by August to ensure the Americans would run the occupation of the home islands. He already refused a Soviet request at Potsdam for a Soviet postwar occupation of Hokkaido. The State Department via the State-War-Navy Coordinating Committee (SWNCC) in the meantime had drafted SWNCC 70/5, viewable here, on 13 August which outlined much of what emerged postwar as SCAP. This document was the culmination of thinking within the State Department which stretched back to 1944 in which the occupation of Japan needed an American control that was unquestioned. SWNCC had a leg up on JWPC-385/1 in that MacArthur's staff was already opposed to a zonal division and had a preexisting contingency plan for occupation of the home islands- Operation Blacklist- in case Japan suddenly collapsed. So the State Department had a very powerful ally within the Pacific theater to argue against the Pentagon's JCS factions favoring a zonal division. Truman ultimately sided with the State Department and SWNCC 70/5. Truman had made his decision known by late August 1945 and endorsed the SWNCC plan for Japan.
While SWNCC 70/5 was a plan for American domination of the occupation, the plan itself did not outright make such a bold claim. The plan did say that a "major share of the effort in the war against Japan has been, and will continue to be made by the United States," but it framed American control of the occupation as a logical military necessity. Truman at Potsdam and in internal memos asserted the necessity of unified command, unlike the Four-Power arrangements in Germany and Austria. Moreover, the president and the Americans also made it clear that any Allied nation could participate in the occupation if it desired to do so. Truman was keen at Potsdam to get China on board with this plan, but the only real takers for what became SCAP was BCOF. The Soviets of course would never countenance to having a subordinate military position to the US. But for all the claims of SCAP acting on behalf of the Allied powers, it was clear to all concerned this was an American operation.
This begs the question of why the other Allied powers relented to this state of affairs. Both the early Cold War and the suddenness of the Japanese capitulation greased the wheels for implementing an American occupation. The fluidity of the situation gave the Americans an edge in that they already had a clear agenda of what they wanted in a postwar occupation (at least as far as which country ran the occupation). The other Allied powers were much more divided and preoccupied with other issues. For the Western European Allies, reestablishing imperial control over colonies taken over by Japan was of greater importance than occupying Japan itself. The ROC leadership generally showed little interest in Japanese occupation, but was determined to retrieve Taiwan from Japanese control. Both Stalin and Molotov argued for a Soviet occupation of Hokkaido or a joint US-Soviet command of SCAP, but they did not really push this issue. For one thing, although the US was adamant against a zonal division, US diplomats were more flexible with the Kuriles and Sakhalin issues. The Americans likewise agreed to a zonal arrangement in Korea and the Soviets were able to wrangle railway concessions in Manchuria and the Liadong Peninsula. So while Truman closed off Japan to the rest of the wartime Allies, the American attitude towards the rest of the Pacific basin was much more flexible.
Sources
Barnes, Dayna L. Architects of Occupation: American Experts and the Planning for Postwar Japan. Ithaca: Cornell University Press, 2017.
Iokibe, Makoto. Diplomatic History of Postwar Japan. Oxon: Routledge, 2013.
Takemae, Eiji. The Allied Occupation of Japan. New York: Continuum, 2003.
Trotter, Ann. New Zealand and Japan, 1945-1952: The Occupation and the Peace Treaty. London: Bloomsbury, 2012.