Until reading this recent article in Japan's Mainichi Daily News, I was unaware that US military bases in Japan are not subject to any environmental regulation. I've become familiar enough with how the US military conducts business in US territories that this didn't entirely surprise me -- but how could a first-world, industrialized, independent country like Japan allow unmitigated environmental contamination on its own soil by the US military?
Part of the answer may lie in the simple fact that the US/Japan Status-of-Forces agreement was signed in 1960, based on the Japan-U.S. treaty of mutual cooperation and security - back when environmental regulations weren't top of mind. (And far from being popular with the Japanese, the treaty was, in fact, violently opposed by many in the Japanese Diet; mass opposition riots even led to the resignation of Japan's Prime Minister, Nobusuke Kishi. The treaty only passed by default, when Japan's House of Councillors failed to vote on the issue in time.)
As to why no one has bothered to amend this agreement in the intervening fifty years and add in some environmental protections - that answer may lie in the simple fact that the vast majority of US military bases in Japan are located in Okinawa. While Okinawa has been a part of Japan since 1879, and is represented in the Japanese legislature, the Okinawan people have a distinct language and culture from the rest of Japan. Many Okinawans feel that they have been colonized -- both by Japan and, with Japan's blessing, by the US military. Okinawa was, in fact, under US administration for 27 years -- from 1945 until 1972 -- meaning that, technically, all those Okinawa bases weren't part of Japan when the Status-of-Forces agreement was signed in 1960. And the Okinawans have, until recently, held little political power in Tokyo.
The good news is that the new Japanese government is finally paying attention to the Okinawans. And getting the US military to take responsibility for the environment it operates in is one of the bargaining chips being put on the table. The question now is, will Washington pay any attention?