Probably because Sega is the publisher? Shouldn't this be clearly communicated on the store page?
Unless it is and I'm blind...

Game is available in Japan.
Only not included are Japanese language.

<See screenshot>

I am in Japan and it doesn't show for me either.

EDIT: Support just confirmed it is region locked in Japan.

Sad if this game isn't supported in Japan.

Probably best way is to find someone out of Japan (maybe a friend) to send the game as a gift code.

No, this isn't possible.
The store is region locked, which means that if you reside in Japan and the way you paying is also registered in Japan the purchasing and payment is prohibited by the account of the GOG store which is region locked.
I am afraid there is no (legal) solution for the residents of Japan.

Yeah, I tried to buy it with the discount since my only copy is on an ancient dvd in another land, but can't because I'm in Japan as well.

Can't make sense of this one, at least with Red Alert 3 on Steam, I can vaguely understand why that was never released in Japan, but this is a major WTF.

So you're saying the game can't be bought by somebody outside of Japan and gifted to somebody inside Japan?

I am guessing since buying Alpha Protocol is prohibited inside Japan, it may be possible to buy externally and gift --> to someone living inside Japan.

Hold up, I just checked the files for the game.
It has localization files in the Engine folder, is there something in it that wouldn't have flown in Japan?