84Goji4Ever,
A part of it that's very similar may have been used. But that scene was void of the first part of the theme and it was slower in the scene you specified.
The track is actually closer to a variation heard in Godzilla and Mothra: The Battle for Earth, but it doesn't quite match the Mt. Fuji scene either. It might just be stock Ifukube as used over the years as well.
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