Historic Temples of Japan: Toji Japan's Tallest Pagoda. Toji once guarded the gates of the ancient capital of Kyoto. Today, Toji is an oasis of serenity in the middle of a 21st-century city. Most temple complexes include at least one pagoda, which is the Japanese version of a stupa. A traditional Japanese pagoda has either three or five stories and is used to house a relic of the Buddha, or at least something representing a relic. It is the tallest wooden tower in Japan.