Not at the moment it isn’t, if you think about it in fundamental and relative terms. Right now Japan needs to pay off a lot of things, both which are coming from bills domestic and abroad. And a stronger currency will help them pay things off faster; and it will put the country in better shape for the long run.
Right now exports and business operations come second in Japan. They need to first repair and startup a lot of their infrastructure. People there also need to spend money domestically to rebuild and continue their lives. Currency must have as much positive effect as possible. So having a strong currency right now for Japan is a great thing. The media and the corporations do not put the responses to this in that real perspective.
Once the situation starts to get more under control and things start to get back on track, the currency value will correct its self in the right time; which is obvious when that it.