I can name hundreds in Scotland, starting with all the ones in Shetland, the Orkneys and Outer Hebrides, that are more than 50 miles from a city. And that's allowing for Inverness being a city, when it's kind of the size of Loughborough, maybe smaller. (Very pretty though. It's my favourite UK city. Been there many times )
Honshu, the largest of the Japanese islands, is 800 miles long. Tokyo is roughly midway, with Nagoya about a quarter, Osaka at the southern end and Sendai is on the northern quarter. All cities of 2m+, north of that, no huge cities, but many about the size of Leicester or Coventry.
Whilst I imagine there are remote parts of Japan, I expect they're for similar reasons to the UK, remote islands.