I don't know about Japan, but numbers in ancient times were used to count items, animals, money etc. so a lot of concepts usual to us (like zero, negative numers) were not accepted. Imagine a negative amount of money for example (later though it was used to represent debt). Unlike negative numbers zero wasn't accepted for a while (even numbers like 204 were written like 2 4).
I believe the concept of "zero" comes from Arabian mathematicians, so although the term is borrowed from the English (actually, English takes it from the Italian zero, which takes it from the Arabian/North African concept of "zefiro", prior to the mathematical discovery (or "invention," really) of the concept of zero, no one really had a concept of "0"
There's the kanji, 零, that is pronounced れい. Sometimes they use a circle kanji (〇) which is also pronounced れい. But ゼロ is much more common than both. However, you might find the kanji 〇 with other kanjis, like for example, a telephone number could be 五六四・三〇七・二〇九〇 (564-307-2090).