Originally, the agreement was to be signed next week, but the actual signing may be postponed due to concerns that it might hinder the progress of the six-party talks on North Korea's nuclear arms programs. We don't want to give Pyongyang an excuse to back out.
From the Joongang Daily:
The defense meeting comes after years of expectations that such an agreement would be signed. In 2003, President Roh Moo-hyun and Prime Minister Junichiro Koizumi agreed in principle to reinforce Seoul and Tokyo's military cooperation. A similar promise was made when South Korea and Japan announced a partnership declaration in 1998.
So far, according to military sources, Seoul and Tokyo have been cooperating in areas of intelligence sharing over Pyongyang's nuclear arms programs and missile systems and in joint search and rescue operations carried out by the South Korean Navy and Japan's Maritime Self-Defense Force.
Despite all kinds of talk in the conservative blogosphere that South Korea is practically in China's and North Korea's camp, thanks in part due to gaffes by the South Korean president himself, the reality of what South Korea does with Washington and even Tokyo shows that Seoul is far closer to those two than to Beijing and Pyongyang, and that's not likely to change.
According to a Japanese source, South Korea will be only the second country with which Japan has signed a military exchange accord. The same source said the following: "To cope with changes in Northeast Asia, such as China's growing military presence and North Korea's nuclear issues, closer ties between Seoul and Tokyo are vital."
This also represents, I think, a return to the pragmatism employed by former President Kim Daejung. The Joongang Daily quoted a South Korean official: "There are pending diplomatic issues such as the Tokto territorial dispute with Japan, but it is necessary to bolster our military relationship with Japan."
I have said it many times, and I will say it again: while there are some legitimate beefs between the two countries, South Korea and Japan have far more in common socially, economically, and politically with each other than with any of their neighbors, and those beefs should be resolved but never allowed to derail what should otherwise be good relations between these two nations.