No, that's only Ise Shrine, which is famously rebuilt every 20 years using what's basically a blue/green deployment: build new exact copy next to active site, switch over, tear down the old one, repeat.
The reason there are few really old buildings in Japan is that earthquakes and WW2 destroyed almost all of them. That said, Kyoto and Nara do have numerous 300+ year old buildings like Todaiji, which also remains the world's largest wooden structure.
Not to mention various other wars and random fires, such as the Ōnin War 応仁の乱 in the 1400s, a civil war between many feudal lords, which destroyed much of Kyoto among other areas.
The world's oldest extant wooden structure is the Kondō (main hall) of the temple Hōryū-ji 法隆寺 in Ikaruga, in the Nara Prefecture of Japan. It was initially built in 607 but completely burned down due to lightning. It was rebuilt in 670, but again nearly burned down by accident in 1949 [1].
It's interesting to contemplate how across these timescales war, disasters, and accidents make it so difficult for structures to survive.
And fire. The thing with buildings made out of kindling is that they tend to burn down after a while whether that's intentional or simply because lightning happened to strike in the wrong place, or these days the man-made equivalent: electrical faults.
The reason there are few really old buildings in Japan is that earthquakes and WW2 destroyed almost all of them. That said, Kyoto and Nara do have numerous 300+ year old buildings like Todaiji, which also remains the world's largest wooden structure.