If the missile was fired at Alaska, the GBIs based in silos there would have a shot at it (as it approached Alaska, not over Japan) The GBI has barely been tested under real-life conditions, but it is physically capable of the interception.
The issue isn't mostly the range of the trajectory, it's the acceleration and geometry of interception in boost or early mid-course. You need a truly enormous, very fast,very expensive missile - which the long-canceled Kinetic Energy Interceptor was.
The Aegis SM-3 Block II which has an IOC of 2018 has a shot at ICBMs in early midcourse. It will be the first missile so big it completely fills a strike-length VLS cell top to bottom, side to side - SM-3 can't get bigger after that without new ships/new VLS.
So until 2018 the Japanese can't do jack squat about any ICBMs flying over Japan.
The Japanese PAC-3s already exist so it isn't a big deal to "deploy" them. And any statements about them probably refer to intercepting a failed ICBM (which is a high probability) that happens to fall towards Japan.
All of this is basic physics known to all/open-source/unclassified, btw.
An SM-3 took out a satellite in orbit in Burnt Frost in 2008, don’t forget.