"は" is the topic marker and is used to mark the main topic/subject of the sentence, which in your case here is Japan. A lot of learning resources suggest that は can be thought of as "As for..." so you could think of 日本は （にほんは） as "As for Japan..".
The particle が marks the subject of the sentence and is slightly different from は although of confused. You can read more about it here.
The particles で and に have many usages chiefly though, で is used to mark a method or means by which something is done e.g. 車で行きます。(I will go by car), or the place in which an action takes occurs so it wouldn't be right here. As for に, I am still not sure on when to use it correctly all the time but many times, it marks the direction in which an action occurs/the indirect object of the sentence. So it would be wrong here too.
Thus, the sentence translates to "As for Japan, the prices are high" i.e. "Japan is expensive". Hope this helps.