The trouble with these surveys is that if you read the fine print they compare COL for ex-patriate executives. Their assumed style of life and expenses are a lot different than most peoples so they are not a good indication of the real costs in these cities.
I can assure that yes Tokyo is expensive but no way is it more than London or New York. One example, try getting a fair sized 2 bedroom apartment in NY for $1200, that is what a nice one costs in Tokyo.
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