Japanese had a long tradition in masonry architecture. This paper discusses the design of a pagoda built in 711 AD (it was in fact rebuilt since the even older prototype perished in a fire). Thus, the earliest earthquake-resistant structure was built in the 8th century or earlier. However it was not before the 1870s when Japanese started working on universal earthquake engineering codes.

In a 1891 Ms 8 earthquake, Japanese structures resisted well but English structures were destroyed. It is reasonable to assume that at any given time the mean age of structures in an area is well longer than 20 years, so we should assume that buildings constructed before 1870 were already resistant enough (or that English had no idea about earthquake engineering, which is likely, although the earthquake was very large). This implies that a tradition was already in place and it's not unreasonable to assume that this tradition goes back centuries if not millenia. For more details a Japanese should answer.

EDIT: A book discussing Japanese earthquake engineering, with some emphasis on the 1891 earthquake.