Many, many scholars would refute the idea of Japanese collectivism. It's really an idea that's touted by Western media, obvious in all the papers when they refer to Japan compared to Western countries. It's just bias.

Here's the abstract to a paper that seeks to refute it.

To assess the validity of the dominant view that the “national character” of the Japanese is more collective than that of the Americans, this paper reviews ten recent empirical studies that compared these two nations regarding individualism/collectivism. Two experimental studies on conformity and five questionnaire studies found no substantial differences. Two experimental studies on cooperation and one questionnaire study found that Japanese college students were more individualistic than American counterparts. The only study that supported the dominant view (Hofstede, 1980) is found to have little validity because its “individualism factor” is virtually unrelated to the common definition of individualism/collectivism. It is shown that the past collective behavior of the Japanese can be interpreted as a universal reaction to the international situations that required cooperation inside Japan and have recently changed drastically. A review of the past literature that produced the dominant view suggests that it was formed through the fundamental attribution error and other judgmental biases.

If you're able to read Japanese, the article is right here. This directly contests with Japanese collectivism and is a more empirical study.

About the rice farming -- I'm not sure. I never heard that before. But, remember, there are a lot of other communities in Asia that were primarily based on growing rice. I don't think they have as much of that "collectivism" thrust upon them as Japan. Growing rice is just something that's extremely labor intensive and needs to be done in a group and not exclusive to Japan.

I wouldn't it say it was the most rebellious either, but there was a lot of activity (but to expand, they are one of the few countries that's never been colonized). National identity didn't really exist pre-Meiji era. That nationalism was "created" with Meiji society as a way to face impending Western imperialism/invasion and rebuild a stronger, more united country. Remember, pre-Meiji was the times of the Bakuhan system - compared to other nations at the time, it could be seen as the least collectivist because they were split into individual, little hans that barely paid heed to the bakufu. There wasn't a strong national identity pre-Meiji period. Could hardly be considered a collectivist group.

And, during the Taisho, right after the Meiji, there were plenty of dissenters who wrote out against the government. It wasn't universally accepted. However, the Peace Preservation law ended that. Tenko was the process conversion of dissenting opinions by forcing them to acknowledge that imperial project and (resign?) their old beliefs. Post-Taisho, the government tried to make sure that the people were completely wrapped in the imperial project for the war time effort. There were of course people who weren't completely convinced, there would always be people like that - but the majority was obeying the narrative that the government and media spun for them.

Skipping deeper into the Showa period, it was undoubtedly a little different due to the period of High Speed Growth, where there was a strong emphasis on working together to continue Japan's unprecedented economic growth. There was also a business idea that the cooperation is like a family and you are loyal with it and time/experience gives you benefits. It's understandable, maybe, with a strong emphasis on nationalism, this unwavering loyalty to one business, visitors/reporters would see as collectivism, in a way, there was. High speed growth, this rise from the ashes, Japanese people felt proud about their status.

But the Heisei is after the bubble burst. Freeters (people jumping around jobs, like freelancers) and this counter culture emerged. There's actually this disconnect between the previous generation and the current. Old ideas aren't working anymore and Japan is actually in for change. It's not as homogenous as it might appear, especially now. Look at all the "weird" culture that's appeared, the older generation is a bit appalled by the youth.

The collectivism might have been a result observations of the Showa period, maybe the Meiji, but Japan isn't this group of people. As my TA points out, the north and the south can barely understand each other because of dialect. Especially now, with all the troubles Japan is facing, that national identity is wavering. Yet, our media still refers to them collectively. It's a bias.

edit: conquered is the wrong term as pointed out. i mean colonized

Their identity is not unified across the archipelago. Two important groups come to mind: the Ainu and the Okinawa.

The Ainu people of Hokkaido were conquered, subjugated or oppressed for extended periods of time in the history of Japan. Today, they are a somewhat protected minority in modern Japan, but relatively few remain. They were subject to all sorts of mistreatment and forced assimilation over time, but I am not familiar with the details.

The people of Okinawa (previously Ryukyu) were a sometimes independent, sometimes subject kingdom in the Ryukyu archipelago south of Japan. They enjoyed trade rights with China as well as Japan in their late history. This made them unique, as the rulers of Ryukyu swore allegiance to the Chinese emperors and the Japanese (after an invasion in 1609, they were considered vazals of the Shimazu clan, which ruled Kagoshima/Kyushu) at the same time, who during the Sakoku period (a time of extreme isolationism) did not trade directly. The Japanese encouraged this deal, and Japanese officials supposedly hid during visits from Chinese officials, as Kagoshima made a lot of profit marking up Chinese goods for resale to the other Japanese.

The Ryukyu archipelago was also the only place in Japan where sugarcane could be cultivated, and the rural population were treated as de-facto slaves: they were forced to cultivate only sugarcane, and currency was not allowed on the islands. Instead, they had to pay for everything (including food, which they were prohibited from farming themselves) using sugar, at prices set by their Shimazu overlords. During various conflicts, some as recent as World War 2, the Okinawans were poorly treated by Japan and used as a bargaining chip with China, and to this day the Ryukyu "natives", which make up a large portion of the population of Okinawa prefecture, speak a distinctive dialect (called Okinawan Japanese) and have strong resentment and distrust towards the central Tokyo government.

Exploiting the Ryukyu population for sugar and Chinese imports made Kagoshima one of the wealthiest domains in Japan, and the islands were incorporated into imperial Japan following the Meiji restoration, after which the population was subject to a range of assimilation measures issued by the central government.

The idea that "Japan" or "East Asia" in general is exceptionally collectivist is rather misleading. This thread has some really good discussion in that regard.

To focus on Japan in of itself however, I would reject the idea that it has anything to do with "rice farming." While certainly rice requires significant amounts of aggregate labor in order to farm properly, the Japanese also grew and consumed many other agricultural products as well. To give a modern example, Udon noodles (made out of wheat) were popular from at the very latest the Edo period (1600s) which is about comparable to the spread of the potato in Europe. Soba noodles, or at least buckwheat, were cultivated at least from 900 AD. For the matter of rice, if the rice is processed or dehusked (i.e. white rice), it deprives the rice of certain nutrients that, if not supplemented with other sources (like buckwheat) one may end up suffering from the nutritional ailment of beriberi, which was a common illness as recently as the 1940s with the Imperial Japanese army, although that had mostly to do with the poor logistical chain (if it could be called that) that failed to supply their troops properly.

If you don't mind, I would like to rephrase the question, because so far the answers seem to be focusing on the "collectivist" bit which is somewhat perpendicular to the main question.

Whether or not all Japanese people are alike, of course they aren't, or whether or not there is regional variation, of course there is, Japan does not have the sort of constellation of ethnicities one can find in, for example, SE Asia. The Japanese Yamato identity is dominate across the island chain outside of a few pockets of Ainu identity in the north, and the Ryukans. How did this come to be?