Rather than conform to the typical concept of heroes, who are commonly measured in terms of how much damage they inflicted versus their personal risk, this list aims to go some way to rectifying this by briefly introducing some examples of Japanese heroes that put the wellbeing of others before that of their regime.
Toyohiko Kagawa was a Christian reformer and activist who deserves mention for his sense of humanity during the peak and fall of Imperial Japan. He showed his Buddha/Orwellian side by abandoning the luxuries of modern Japanese life to experience poverty in the slums first hand.
That might not sound like much, but Kagawa went through a good deal of persecution in Imperial Japan, both from the police and his countrymen. Despite this, Kagawa set up the Anti-War League, and publicly apologised to China for the invasion. For this, Kagawa was arrested and briefly imprisoned.
It's this kind of selfless, righteous* tenacity that epitomises true pacifism.
Sugihara contacted Japan several times, and failed in all cases to obtain permission to provide the visas, but after some contemplation decided to write the visas anyway. With the visas in hand, many thousands of refugees were able to pass through the Soviet Union and Japan, undoubtedly saving their lives.
Sugihara is fairly well known in Japan, and by numbers alone Sugihara should be at the top of the list, but I've given him the number two spot. Why? As much as he was a Japanese national, his only act of antagonism towards Imperial Japan was writing the visas, which you might argue was a dangerous thing to do; however I'd question the likelihood of Imperial Japan to go so far to persecute him. More than anything, I'd describe Sugihara as a hero of Europe, rather than Japan.
FYI, here is an essay of spectacular scope** regarding Sugihara: informative link.
Nevertheless, one might argue for Shidehara's heroism in the face of the assassination attempt on his contemporary by ultranationalists, and its this argument for which I include him in this list, even though there is much more to talk about regarding Shidehara.
Takagi's ability to evaluate Japan's position in the war lead him not only to realise the inevitability of defeat, but to conclude that peace must be made with America, and that to do so the Prime Minister (Hideki Tojo) must be assassinated.
Knowing Tojo to have a great affection for open-top cars, Takagi planned to barricade, or block the Prime Minister's car, then open fire using a machine gun. The plan might have succeeded, considering Takagi's powerful supporters, however the plan was never invoked due to a mass resignation within the Tojo cabinet over the loss of Saipan. Takagi spoke later that "Had the assassination taken place, the resulting increase in tensions between the army and navy would have made peace-making difficult"***.
Unable to carry out the plans, Takagi still worked towards a peaceful end to the war, though as evidenced by the near-destruction of Japan, his efforts were not entirely successful. Nonetheless, I think Takagi's powerful resolve, which would likely have gotten him killed had it been exposed, earns him a place in the top 5.
Nosaka joined Comintern and eventually was ordered to help China's resistance to Japan. This lead to Nosaka helping in the indoctrination of captured Japanese troops. Apparently, he was so successful that the Japanese army made attempts at assassinating him.
In this light, Nosaka appears the very embodiment of heroic resistance against Imperial Japan, but as the Wiki points out, there are a number of darker aspects to Nosaka's career.
Firstly, it was found that Nosaka had close ties to Stalin's regime, worse, it appears he used that position to exact personal vengeance on his friend after hearing they may have slept with his wife. The alleged adulterer was ultimately killed by firing squad.
Secondly, there is the fact that he was working under orders from Comintern. I'd like to think that Nosaka was working to mitigate the evils of Japanese occupation of China, but I wonder to what extent this was just to further the communist cause. That is to say, was Nosaka aiding the Chinese people, or just trying to impose his own world view?
Whatever the case, Nosaka highlights the fact that some Japanese soldiers, when educated on the evils committed by Imperial Japan, were happy to take up the cause of the Chinese. A fact that seems entirely overlooked in the popular memory of the war. In this light, even if Nosaka's own heroism is vague and tainted, I'd like to think that perhaps he produced a few heroes, no matter how they may have faded from history.
*I'd like to stress that I say righteous here without any invocation of mythical/theoretical beings
**at least in terms of what is freely available on the internet
***information from this paragraph can be found in Japanese here