I don’t see what the big deal is about this so called secret agreement made with Japan nearly 60 years ago:

In a 1958 secret agreement with the United States, the Japanese government effectively ceded the right to try U.S. military personnel for crimes committed in Japan, Foreign Ministry sources said Saturday.The revelation comes on the heels of reports of the existence of several secret security-related agreements between Japan and the United States.

The latest revelation came to light as a result of a ministry investigation into the matter, according to the sources.

The de facto abandoning of jurisdiction over crimes committed by U.S. military personnel was referred to in a document on Japan-U.S. talks held in connection with a bilateral Administrative Agreement signed in 1952 regarding the status of U.S. military installations and members of U.S. forces stationed in Japan.

The agreement was replaced by the Japan-U.S. Status of Forces Agreement at the time of the 1960 revision of the bilateral security treaty.

The 1952 agreement stipulated that Japan could exercise jurisdiction over criminal offenses committed in Japan by members of the U.S. armed forces while not on official business, though offenses committed on duty should be under U.S. jurisdiction.  [Stars & Stripes]

This would be like announcing a secret pact between the US and Afghanistan 60 years from now complaining about US soldiers not being tried in Afghan courts.  This is another example how the Hatoyama government in Japan is the second coming of Roh Moo-hyun.  The Korean left while in power had a fixation on GI crime as well and now that the Japanese left is in power they got to have the same fixation.