Distance

When you live in a huge metropolis like Tokyo, most people get around on public transport instead of cars. What this means is that properties closer to the local train station are much more expensive than those further away. Land is at a premium and it also means car parking is also very expensive!

Prices also change depending on what train line the property is nearby. For example lines like the Yamanote line are extremely well connected and popular, so properties nearby Yamanote line stations will be a lot more expensive than those nearby a less major train line. 

If you own a car and are perfectly happy with living far away from the train station, or central Tokyo for that matter, you'll be likely to get a much bigger better apartment for the same price of a tiny apartment near the station.

Now for real estate standards "close" to the station is usually considered to be a 10 minute walk or less, with 5 minutes or less being considered extremely close. However when it's a major train line like the Yamanote, you can still expect to pay a premium for properties that are a 10~20 minute walk from the station.