Do official health agencies recommend getting the "Japanese Brain Fever" vaccine for travel to Japan?

The French governmental website "advices to travellers" says about Japan (my translation):

For long stays in rural zone (and at some seasons), vaccinations against 
hepatitis A, B, typhoid fever or japanese encephalitis can be advised.

Just thought I'd give a U.K. perspective.

You almost certainly don't need the vaccine, particularly if you're visiting soon - the transmission season is June - September, except in Okinawa / Ryukyu islands where it's April - December.

I was advised by the gap year charity I went to Japan with to get these vaccines, but my doctor informed me that they were unnecessary (for Tokyo).

More specifically from the U.K. Government on who is at risk:

JAPANESE ENCEPHALITIS: ... Short-term travellers and those who restrict their visits to urban areas are at very low risk. Those at higher risk are travellers who visit or work in rural agricultural areas such as rice fields and marshland. Long-term travellers and expatriates are also at higher risk.

and on risk management procedures

Travellers should take mosquito bite avoidance measures. Culex mosquitoes feed predominantly during the hours from dusk to dawn. Vaccination should be given to travellers whose planned activities put them at higher risk (see above). There are specific contraindications and adverse events associated with JE vaccine. A careful risk assessment should be made before administration and specialist advice sought as appropriate.

From The National Travel Health Network and Centre, part of the U.K Health Protection Agency.