This seems like such a minor thing in the scheme of things:
The deployment, to Yonaguni Island, is part of a general trend of transferring forces from Japan's northern flank to the extreme southern flank. Aside from a small contingent on Miyako Island, the southern islands have been totally demilitarized and vulnerable. The establishment of a so-called coastal monitoring unit can be seen as a means of asserting Japanese sovereignty over islands in a region of conflicting claims.
The decision to install a 100-man unit, estimated to cost ¥1.5 billion (US$20 million) and expected to be completed by 2015, is part of a growing trend by the nations that surround China to tighten up their defenses as they increasingly side against what they perceive as the growing belligerence of the region’s biggest country.
Yonaguni, only 28.8 sq. km in size and with a population of 1,700, overlooks the 300-km gap in the so-called First Island Chain, a maritime line running between Japan, Taiwan, the Philippines, Vietnam and Indonesia – all of which would potentially side with the US in case of war with China. If the situation were to turn sour in the West Pacific, it's the Miyako Channel where the US, Chinese and Japanese navies would likely grind together.
The Chinese are angry. As one analyst notes, anti-ship missiles here would be a potent threat to Chinese ships trying to head east to blue waters.
Taiwan is also a bit annoyed since this cements Japanese control of an island that Taiwan contests, but this will help Taiwan. The anti-ship missiles are obvious. Anti-aircraft missiles will also help secure supply lines and routes reaching from Japan to Taiwan, and will help screen American forces moving into the western Pacific (which the analysts also raises in the context of anti-ship missiles deployed there). Radar on the island would help Japan and America cover the Taiwan area and make our intervention more effective.
This is part of Japan's long-range plans to shift forces from a Soviet-era northern focus to a China-focused southern deployment. China doesn't like this one bit. But as long as we stay committed to the region, countries can live with China's anger.
China thinks that their growing power means the region can go back to treating China as the middle kingdom around which they must orbit, but China's neighbors have gotten used to not being tributary nations and don't want that old business as usual one bit.
