Until recently, the three services of Japan's "self defense forces" have been strictly autonomous. There was no such thing as "jointness" and each service chief reported directly to the civilian leadership. This situation was the result of a deliberate decision to avoid "unification" of the armed forces, given the country's history of militarism. This despite the extraordinary state of inter-service rivalry between the old Imperial Army and Imperial Navy. This is about to change.
The Self-Defense Agency, the equivalent of a Ministry of Defense, recently created the equivalent of a "Chairman of the Joint Chiefs," and this officer will shortly take "command" of all three services. The long-term goal is to integrate as much of the administrative side of the self-defense forces as is possible, including procurement, logistics, and so forth. For now, however, the authority of the "chairman" will be limited to operational matters, under the watchful eye of the Prime Minister.
This is an extraordinary, and long overdue, reform. During World War II, and before, the army and navy (there was no independent air force) would regularly refuse to cooperate, even when the lack of cooperation hurt both services. Each service, for example, had its own fleet of cargo ships and tankers, and would not coordinate their use, letting ships return empty, for example, rather than move some material for the other service. Both services often developed plans that contradicted each other, even through both services were on the same islands threatened with attack by the United States. There was more cooperation post-World War II, but not to the degree that was required to make the most of Japan's military forces.