that's not a fair comparison because they are built to different specs. fender japan's factories have the freedom to build their their basses to whatever specification they choose, and in terms of construction and finish, it differs from the MIA models. the most notable recent development is the choice of dimarzio collection pickups and USA vintage pickups, both of which are built specially for fender japan and do not exist elsewhere. i think the story now is that japan builds copies (not reissues) of vintage basses, while usa comes up with the innovation.
japanese-market models do not exist anywhere else in the world. MIA models are named such as fender american deluxe, while japanese models are named such as JB62-DMC. the only model that is common to both japan and the rest of the world, although with different model names, is the jaguar bass. that is because the jaguar and aerodyne sold everywhere in the world is produced in japan.
it is also becoming an increasingly common practice for fender to discontinue and introduce new models in their line. fender japan recently revamped their entire range in around april 08. fender USA is also known to shuffle the pack, such as the brief use of the S1 switching, for example.
there are alot of theories as to why fender USA costs so much more than anything else. to me the most logical and plausible reason is due to fierce protectionism in japan. you may find it surprising but the japanese market goes crazy over american-made guitars, such that they are willing to pay large sums for their gear. a rickenbacker 4003 costs as much USED in japan than it does brand new in USA. a EBMM SR4 lists for 1.9k (list) 1.3k (street) in USA, while it costs over 2.1k in japan. the difference is too much to write off as a result of shipping.
but that is given today's exchange rates. in the 80s during the height of japanese industrialization and before the property market in japan crashed, the Yen was extremely strong against the US dollar. as a result US made guitars became dirt cheap for the japs.
the only way for fender japan to compete with american guitars was to cut prices. these prices were only meant for the japanese market, given the circumstances, and not for the rest of the world. in april 08 fender stepped in to restrict exports.
this is only my interpretation of the events, and most people would think that it was the other way around, that the americans were fighting off japanese imports. but it made more sense to me this way. but it's all good with rock and roll because these theories can't be proven.
you can read alot of other opinions in the gear-guitar subforum, where it has been discussed in great depth, and the difference between CIJ and MIJ is spelt out (you can find an article of it on wikipedia as well)
