That article about "fleeing" Tokyo has become a bit famous around the net as an example of extremely misleading, fear mongering journalism... Not to mention irresponsible. It has been reported numerous times to journalism authorities, and right now there is actually a movement to get them to remove the outright fabricated title.
The government has been planning on a secondary base to move the government to in the event of a catastrophic event for the past 30 some years. Every country has these plans. Japan has not suddenly started looking into this after the earthquake or for reasons to do with radiation. It is a normal government thing to plan for a situation where the capital is no longer able to be used safely.
There have been various candidates put out on the table of the past so many years, but they don't like to actually make their plans clear lest the new base of operations be put in danger also in a war situation.
I would be flat out shocked if there was any country out there that did not have plans in place for what to do if the capital suffered a horrible event. It would be stupid not to.
What is even more pathetic is that there wasn't even any new movement related to this. Journalists dug up the simple fact that the Japanese government has a "backup" plan for a new capital and decided to make it into a sensationalist story.
Out of REAL news, I guess.