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Yes, but the situation got a lot better and a lot worse...

Sadly there has been a bunch of pretty devastating earthquakes in recent years. In particular in Kumamoto the one in 2016 (magnitude 6.5) was huge and many of the houses built at lower standard or not in great shape anymore got partially or totally wrecked. Right now the house that are left are relatively well built.

The bad news is, that still doesn't help as the cumulative damage can still bring them down, and they're still subject to landslides, water damage, and other second order disastrous events.

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Earthquakes didn't start in 1991. The Japanese have always had to live with earthquakes and build accordingly.
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For a long time "live with earthquakes and build accordingly" meant "make it easy to rebuild", not "engineer the structures to withstand the earthquakes".
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In Gölcük/İzmit, there was a huge 7.4 earthquake in 99.

https://en.wikipedia.org/wiki/1999_%C4%B0zmit_earthquake

It took around 10 years until the city felt "normal" again (source: a close friend lives there).

My point is, it's never easy to rebuild.

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The regulations got hardened in 1991. Obviously there has been earthquakes forever, but the buildings were not built to withstand them. That's one of the reasons why Japanese do not buy old homes: they are not earthquake proof.
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One of the reasons Japan uses wood for construction is that combined with their traditional building techniques it results in earthquake resistant buildings.
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