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I have found some GIS data for Japan but the location attributes (prefecture, city names etc) are in Japanese. Anyone know where I could find this data in English, I could get it translated but it would take a long long time.

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    I have worked with some of these data sets, mainly hydrography, and was really impressed by Google translator results – Detlev Jan 10 '16 at 15:15
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OpenStreetMap is another possibility for place names and administrative boundaries (For boundaries, you might find GADM easier to use though, as per Sebastian's suggestion).

OSM uses the name tag in the local language world-wide, but in Japan you'll find many places will have English translations in the name:en tag.

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The administrative units can be found at gadm.org. Some older city names (1995) are at the Harvard Asia Center.

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