According to Wikipedia, Pokemon Red, Green and Blue sold 10.23 million copies in Japan. While it'd be tempting to split that number equally into three and say that Pokemon Green sold 3.41 million copies, the fact that Blue was released in Japan a year afterwards suggests a larger discrepancy than a first-look would suggest. If I had to estimate, I'd say that Green version sold about 4 million copies (along with Red) in Japan. So, it's not 'rare' by any means, but as most of them will be concentrated in Japan, you'd have to use non-conventional means - like eBay - to attain one.