From what I've been told (I used to do research in MRI), it's because MRI's are Japan's preferred method for allowing doctors to show they care.
MRI's are used in Japan the way antibiotics are used in the US. Patients are often unsatisfied if the doctor tell them to go rest and hope things improve on their own (even if that is the best treatment), so doctors perform some harmless token medical procedure to make the patient feel he helped them.
At least MRI doesn't really screw the patient much, and doesn't screw society at all, unlike overprescription of antibiotics.
(I'm in favor of complete availability of most scheduled drugs -- narcotics, pot, LSD, whatever -- but restriction of antibiotics to those with a prescription. Drug resistant bacteria is no joke.)
There's probably some argument for 0.5T MR being diagnostic now, with faster computers. I just think Japan pushed to low-field earlier because they don't actually care about the results. Also Japanese tend to be physically smaller, so maybe a 0.5T there is as effective as a 1T in the land of the super-sized drive-through.
Antibiotics are restricted to those with a prescription in most European countries, for the reason you mentioned. That said, I still keep some in reserve (purchased via prescriptions from doctors in my family) to use judiciously when traveling or living abroad without wanting to deal with the local healthcare system.
MRI's are used in Japan the way antibiotics are used in the US. Patients are often unsatisfied if the doctor tell them to go rest and hope things improve on their own (even if that is the best treatment), so doctors perform some harmless token medical procedure to make the patient feel he helped them.