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Parent comment is about kanji and you’re talking hiragana pronunciation.

Words that may contain kanji that naturally has pronunciations are sorted by pronunciation, yes, but individual kanji never even had an inclusive list and thus no logically defined linear order existed/exist.

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Actually, Chinese characters did originally have a defined linear order (or, rather several schools existed IIRC). It's been a while since I looked at this, but essentially they were ordered by radical and then pronunciation, with some other tie breaker rules. Japanese word dictionaries, though, are indeed usually ordered by pronunciation. Kanji dictionaries have a variety of different orders, but most of them are ordered by radical and stroke count.

All Japanese words (not characters) have kana pronunciations, but yes, for individual kanji characters, people use a specific type of dictionary called kanji dictionary (漢字辞典) and the order of this dictionary is indeed not (always) based on the pronunciation (stroke count of radicals is often used for the paper version).

Here's an (online) example:

https://kanji.jitenon.jp/

On the right hand side of the above site, it shows the pronunciation (both on-yomi & kun-yomi) and the stroke count.

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