I live in a small city in the mountains, and it's much more expensive to fill your tank here than in other places. The rationale for that is the holes in the mountains. Gas tankers aren't allowed to drive through tunnels because of the potentially devastating results of an accident, so to get to cities like mine they need to do some massive detours. This results in an almost 10% markup.
In Tokyo expect to pay around 135-140yen per regular litre right now. Here in Nagano-ken you'll pay something like 142-147. High octane is about 10 yen more expensive, and diesel is around 20 yen cheaper. These figures are liable to change with the economy, but you get the idea.