Kraken, no the waters around Japan are not entirely free to be dived.
The issue is most visible in the diving areas close to Tokyo, but is also seen in other areas to some extent.
It is a cultural, not a legal issue. That said, the two are not always so clearly distinguishable in Japan. The diving thought-leaders strongly believe that there is no legal foundation for the fishermen's argument, however the fishermen strongly believe that the law is on their side. There are many stories floating around, where the local police have sided with the fishermen in disputes with divers. As divers, this is hard to accept, but the fishermen are local comunity members trying to earn a living. They can definately enforce their control over the sea, as they own the boats, can easily disrupt diving operations, and have local support if they need it.
The fishermen believe that the divers' reason to dive is to take fish, particularly shellfish, lobsters and the like. I understand that the fishermen's co-ops do have government granted fishing rights, so they want to protect those rights. Although the number of divers who do take lobsters, shellfish etc is a small minority, the Japanese do love seafood, and there are a lot of divers based in greater Tokyo. So although it is hard to see the fishermen as conservationists, I could be persuaded to consider the argument that if diving was not controlled in some way in Japan, that it could result in an unusual form of over-fishing / environmental damage.
There is also a commercial angle here that muddies the water somewhat. In many cases, dive shops pay an ocean useage fee or boat fee to the fishermen or the co-ops, so sinics might suggest that it is less clear what the fishermen are protecting.
There is one sketchy story floating around of a dive shop that challenged the system through the courts and won, but rumor has it that the dive shop in question was run by an ex-policeman.
The diving industry seems to have a mixed attidude to the issue. On the one hand it does make dive businesses less flexible and more costly. On the other hand, it helps control competion and makes it hard for divers to do their own thing without spending money with the dive shops. I have not heard any view on this rom PADI or other such organizations. That would be an interesting side to hear from.......
Although this might sound defeatist, it is not a battle that can be won without changing attitudes. So my approach is to do what it takes to live in peace & harmony with the local comunity, including the fishermen. Taking a more aggressive stance is likely to drive wedges between the divers and the fishermen and will probably have the opposite effect of that which is desired.
Attached is an excerpt from a work-in-progress guide book that I have been working on for the last few years:
C.