Japan Record Loss
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Record loss in Japan comes from several types of events as it does in many parts of the world. Of particular note is the matter of earthquakes and tsunamis.
War-caused Record Loss
Many times events associated with war cause records to be lost. World War II was a cause of a lot of loss in some prefectures.
According to most accounts of that war, the Tokyo area and Okinawa prefecture had a lot of bombing damage, so many records were lost.
After the war, families that remained reconstructed their family'skosei [Family Household Register] and were added back to their city hall records.
Many from Okinawa immigrated to Hawaii and some reconstructed their koseki record and can be found in Okinawa club records in Hawaii.
Japan is regularly hit by tropical weather systems, so typhoons can cause repositories to be flooded due to rain getting into the building either from flooding from the heavy rains, or because windows were broken. Other storms, such as thunderstorms, also cause damage to buildings housing records. Tornadoes are a virtual unknown.
Earthquakes and Tsunamis
As with every locality that has had earthquakes, records can be lost due to either the damage done by the earthquake itself or secondary events such as fires or collapse of buildings either then or after the main shock. Aftershocks can bring down buildings that withstood the initial shock. Japan is particularly seismically active, residents in many areas of the country experience moderate earthquakes on a rather frequent basis and many say they don't go a month without having at least one or two.
Modern-day building codes since 1980 have made more recent construction more earthquake resistant.
Very strong earthquakes can even topple gravestones in cemeteries, so if you know there was a particularly strong seismic event in the locality of a cemetery, check with the caretakers for the exact location of your ancestor's grave site, and for any information regarding the stone itself if necessary.
If an earthquake occurs off the coast and is strong enough, it can cause a tsunami, which is Japanese for 'harbor wave'. If a tsunami occurs and is large enough, it can destroy everything for some distance inland. Not all earthquakes generate tsunamis and some tsunamis that do result may only be inches high, harmless to any shorelines.
But Japan's history of large earthquakes has also meant there have been at times large tsunamis. So shoreline villages and towns may at times have record loss due to these tsunamis. Two large tsunamis hit the east coast of Japan in the 1850s, following earthquakes estimated as being 8.4 magnitude, two more occurred in 1946 and 1948 respectively, Tokyo had a devastating earthquake in 1929, the Kobe-Osaka area had a 6.9 temblor in 1995, and most recently, there was a magnitude 9.0 earthquake on 11 Marth 2011, that struck northeastern Japan's shore, the wave was over 30 feet high, and in some places went inland as much as 10 km, which is about 6.2 statute miles.
Some shoreline villages and towns probably lost what records they had up to the ti mes of some tsunami events, if the building the locality kept them in was either not high enough above where the wave topped out at, or far enough away from where it went in.
One cannot rule out fires or even careless record preservation in some record loss anywhere, so if you do not find any evidence of records for a locality or a particular time period within it, locate any evidence of some type of event. This is true regarding the other types of events that are the causes of record loss previously discussed.