Step by step, the United States has been increasing its intelligence cooperation with Japan until it is reaching the level long maintained with allies like Britain and Australia. The most recent agreement, to share information on Internet based terrorism and cyber crime in general, allows for the exchange of the most sensitive information. Japan's intelligence operations have been very discreet, but have been increasing since the 1990s (when domestic terrorists made the first, and so far only, attacks using nerve gas). In the late 1990s, Japan reformed its intelligence activities, and created an office (Naicho) that could keep tabs on what Japan's many intel organizations were up to.
With the growing threat from North Korea and China, Japan has put more resources into keeping tabs on its neighbors. There are lots of Japanese businessmen working throughout East Asia, and these provide excellent opportunities for gathering intelligence (even if all you do is chat with these people as needed, and find out what they have seen and heard.) The Japanese have demonstrated an exceptional ability to gather intel in difficult places, like North Korea. In light of all this, it should be no surprise that the Japanese and American spies are getting cozy.