Are you planning on publishing this story or sharing it with others? Because if you're not, than it doesn't matter if it's too soon or not. As long as you're not offended by it and it's for your eyes only, then there's no problem.
If you do plan on sharing with others, explain the situation to them first and make sure they're alright with it. Some people might be bothered by some of the events in the story, especially if they were personally affected by the disaster. But, as the poster above me pointed out, that kind of catastrophe always happens somewhere at some point to some degree, so it's something you always have to be careful for.
If you do plan on publishing it at some point, then perhaps wait a few years before you do, but there is nothing keeping you from writing it now. It could just be that secret manuscript you have hiding in your closet for years until you think the time is finally right.
Although, if you follow the advice of the above poster, don't make unnecessary allusions to the current disaster in Japan, and treat it seriously and tastefully, than there really shouldn't be any problem at all.