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In the Wikipedia article on Japanese architecture, it says in the Heian era, and I quote, "Heavy materials like stone, mortar and clay were abandoned as building elements, with simple wooden walls, floors and partitions becoming prevalent." As someone mentioned, it doesn't give a clear reason for the discontinuation of the use of such materials.

What did Japanese architecture look like with those "heavy materials?" I tried searching things like Jomon and Yayoi architecture, but the buildings look like they're made of wood and straw, and Asuka and Nara architecture looks less obviously wooden, but in the study.com article I will link to, quote, "Most buildings of (the Nara) period were made out of wood, usually painted in red, black and golden colors."

Sources:

Edit: I came across a series of history PDFs by the Japan Lime Association. They're in Japanese, but they could be used as a partial answer to the question of non-wooden architecture in general.

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    Note that stone architecture is in general expensive, so even when used, it doesn't mean that all buildings were stone. The most remaining temples of the Nara era are wooden (en.wikipedia.org/wiki/Historic_Monuments_of_Ancient_Nara) with heavy Chinese influence in style. Even Shosoin, a treasury, was wooden (kunaicho.go.jp/e-about/shisetsu/shosoin01.html).
    – Greg
    Dec 19 '20 at 6:57
  • I think there is an observation issue here: when you read that the building style has changed in Heian or Nara, the change is compared to the previous ages. New building forms like pagodas appeared. These forms stayed, you can see such building around, only they are mainly made of wood now unlike in eg. China.
    – Greg
    Dec 23 '20 at 0:13
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The short answer is mold, tsunami's and earthquakes is why they didn't build with stone. There are few 'ancient' examples of stone building but most of them came from the Chinese style for the temples that were constructed and you can see the resemblance in the Chinese Pagoda vs. the Japanese toba. These Pagoda's were originally constructed as small shrines for a deceased Buddhist's ashes called a stupa and started to gain grandeur and were eventually made into Pagoda's. This is demonstrated in Nara's Hokki-ji (a mostly wooden structure) built during the Nara era it is the oldest Pagoda still in existence.

As for why they didn't build with stone; it goes back to mold primarily. Japan sits in a climate that is high in moisture and rarely drops below freezing in most of the inhabited spaces. You can see that mold, lichen, and moss build up and eat away at stone structures if not taken care of but the biggest problem is the mold making the people inside sick. Japanese used Cypress and Cryptomeria in their construction which like many other woods such as Cedar, White Oak and Teak repel mold and rot. The other portion to the equation is that you can also build your house off the ground slightly allowing for airflow underneath. This also helps reduce mold build up and reduces the amount of moisture in the structure.

This is in great contrast to the granite stone that was being used in the limited stone buildings in Japan. Granite is porous and will soak up and and hold moister making it more likely for mold to build up on it.

The other two reason why they didn't use stone like western cultures is because of tsunami's and earthquakes. As you can imagine, stone doesn't bend and twist like wood can so it shatters during an earthquake which Japan is prone to.

Hope this helps.

References:

https://www.britannica.com/technology/pagoda

https://www.chinaodysseytours.com/chinese-things/architecture-pagodas.html#:~:text=Stupas%20appeared%20in%20China%20with,of%20the%20national%20Buddhist%20art.&text=They%20are%20therefore%20also%20called,and%20are%20objects%20of%20homage.

https://www.nippon.com/en/views/b02314/

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    Is "rarely drops below freezing" really true? While Tokyo summers can be hellishly hot and humid, I've encountered snow in Tokyo both times I went in December. (I'm not disputing the general answer) Dec 23 '20 at 3:32
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    In the northeastern parts of Japan, Tohoku and Hokkaido, "rarely drops below freezing" is definitely not true.
    – RakeALeaf
    Dec 23 '20 at 5:18
  • Not saying that none of Japan rarely drops below freezing. I am just stating that a larger portion of the population centers, especially during the Nara era were in the southern part of the country with average temperatures in January (coldest month) being low 39f (5C) and high of 48f (9C) Note: The Heian Period followed the Nara Period @RakeALeaf
    – EvanM
    Dec 23 '20 at 12:52

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