Why there are multiple pronounciations for one single character in Japanese?

In Japanese writing and reading system there are two different ways to read Chinese Kanji characters: 訓読み (kun yomi) and 音読み (on yomi). Historically kun yomi is used as a way to mark the vernacular words and phrases in Japan with Chinese characters, for Japanese before the 9th century CE did not have their own writing system. On yomi is on the other hand is the pronounciation of the Chinese kanji characters in their own original pronounciation in Chinese. Students have to pay attention in the examinations to the two pronounciation systems, for the same character may change very differently in different occasions in the way they are pronounced.