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The formal German-Japanese relationship in World War II (as part of the Axis) was established in the Tripartite Pact of 1940 (see also Anti-Comintern Pact).
The "Axis powers" formally took the name after the Tripartite Pact was signed by Germany, Italy, and Japan on 27 September 1940, in Berlin. The pact was subsequently joined by Hungary (20 November 1940), Romania (23 November 1940), Slovakia (24 November 1940), and Bulgaria (1 March 1941). Its most militarily powerful members were Germany and Japan. These two nations had also signed the Anti-Comintern Pact in 1936.
Inevitably, theirs was a complicated relationship. This is from Conrad Black's Franklin Delano Roosevelt: Champion of Freedom:
The German invasion of Russia [in 1941] came as a complete shock to the Japanese. The Nazi-Soviet Pact of August 23, 1939, had undercut the former Japanese policy of pursuing a joint German-Japanese anti-Soviet policy and came just as the Russians, under future Marshal Georgi Zhukov, decisively defeated the Japanese in a multi-division "border incident" at Nomonhan.
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As for why the Japanese did not attack the Soviet Union when Germany did, possibly the Japanese were wondering why Germany couldn't have attacked the Soviet Union in 1939 when it would have been useful to Japan. (See Soviet-Japanese Border conflicts .) Japan as it turns out had just signed a Neutrality Pact with the Soviet Union in April 1941, to defuse the tension that had been a result of their 1939 border war, so they could focus on the Pacific. It wasn't in their strategic interest to do an about-face at that point.
The basic problem is that Germany couldn't credibly offer to partition the Soviet Union with Japan, since all the goodies (the wheat field of Ukraine and the oil deposits in Azerbaijan, not to mention the access to Persia) would have fallen in the German half. Japan on the other hand needed to secure oil by taking what is now Malaysia and Indonesia. Attacking the Soviet Union would have been a distraction they couldn't afford.
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The original "Axis" was the Berlin-Rome Axis. When Japan was added, it became the "Three Power Pact."
Even so, Germany had a higher regard for Japan (although Asian) than for its Italian allies. When Japan bombed Pearl Harbor, Hitler exulted, "We cannot lose this war. We have an ally that has not been defeated in 350 years."
At some level, Germany considered Japan part of the Axis (and an "ally") because of shared fascistic and militaristic tendencies. Whether Japan "reciprocated" is a matter of debate. But they considered themselves to have common enemies in Britain and the United States.
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You shouldn't give too much credit to the idea of a coherent Nazi ideology.
One commenter put it: there was no substantial racial theory that would be official in Germany except "Jews are bad" and "Russians are natural slaves" because they are "Slavs" (the words coincide in German)
This is correct. Moreover, Hitler's confused racialism didn't seem to bend any more to expediency than it did to internal consistency. As other commenters noted, Hitler in his unwisdom considered both Chinese and Japanese to be valid races, despite the fact they were at war and he had to pick a side. Contrariwise, he said that the Indians deserved no better than British domination, despite the clear opportunity of using them to undermine the allies.
From Japan's perspective, the Germans were a means to an end. A faction which wanted to attack the Soviets was derided as 'Hitler's office boys', and defeated by the 'southern' faction which argued for an invasion of China. Japan's performance against the Soviets in border clashes had been quite poor.
To Japan, the worst thing about Britain, France and America was that they were nearby. The best thing about Germany was that they were far away.
That being said, Germany and Japan shared intelligence and cooperated to the extent possible. I remember reading on Wikipedia about an incident involving an Italian submarine that arrived in Japanese held waters after the defection of Victor Emmanuel. The crew were out of radio contact and had no idea of the cleavage between the King and Mussolini.
When they arrived, the Japanese hauled them out and made them declare either for the co-belligerent Kingdom of Italy under the control of the Allies, or the Republic of Salo declared by Mussolini. Those that declared for the king were made POWs. That they did something like this suggests they had at least some commitment to the Axis. The path of least resistance would have been just to confiscate the sub and escort all the crew out of the country.
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German racialism was historically flexible enough to accomodate pro-Chinese and pro-Japanese reconfigurations. Japan did not attack the Soviet Union as it was manifestly not in the interests of Japan to do so after the Nomohan incident (see Battles of Khalkhin Gol at the encyclopaedia). Germany did maintain diplomatic and political links with Japan. Some technology transfer occurred, and some trade in incredibly high value strategic goods. The level of coordination and trade was far less than the relationship between Britain and China for example. Yet China is one of the Allies. Propaganda often obscures the real relationships between states.