Proto-Japonic words are generally polysyllabic, with syllables having the form (C)V. The following proto-Japonic consonant inventory is generally agreed, except for the values of *w and *j (see below):
| Bilabial | Alveolar | Palatal | Velar | ||
|---|---|---|---|---|---|
| Nasal | m | n | ɲ | ŋ | |
| Stop | voiceless | p | t | c | k |
| voiced | b | d | ɡ | ||
| Fricative | voiceless | f /ɸ/ | s | ç | x |
| voiced | ƃ /β/ | z | ɣ | ||
| Approximant | w | j /ɹ/ | y /j/ | h /ɰ/ | |
| Liquid | v /ʙ/ | r | l /ʟ/ | ||
It is agreed that the Old Japanese voiced consonants b, d, z and g, which never occurred word-initially, are derived from clusters of nasals and voiceless consonants. The other Old Japanese consonants are projected back to Proto-Japonic, except that authors disagree on whether the sources of Old Japanese w and y should be reconstructed as glides *w and *j, or as voiced stops *b and *d respectively, based on Ryukyuan reflexes:
- Southern Ryukyuan varieties have /b/ corresponding to Old Japanese w, e.g. ba 'I' and bata 'stomach' corresponding to Old Japanese wa and wata. Two dialects spoken around Toyama Bay on the west coast of Honshu also have /b/ corresponding to initial /w/ in other Japanese dialects.
- Yonaguni (at the far end of the chain) has /d/ where Old Japanese has y, e.g. da 'house', du 'hot water' and dama 'mountain' corresponding to Old Japanese ya, yu and yama.
The voiced stops are also favoured by advocates of genetic relationship with Korean and other northeast-Asian languages. However, many linguists, especially in Japan, argue that the Southern Ryukyuan voiced stops are local innovations rather than inheritances from Proto-Japonic.
Most authors accept six proto-Japonic vowels:
| Front | Central | Back | ||
|---|---|---|---|---|
| unrounded | rounded | |||
| Close | i | ï /y/ | ü /ʉ/ | u |
| Close-mid | e | ø | ə | o |
| Open-mid | ɛ | ë /œ/ | ä /ɐ/ | ɔ |
| Open | æ | a | ö /ɒ/ | |
The vowels *i, *u, *ə and *a are obtained by internal reconstruction from Old Japanese, with the other Old Japanese vowels derived from vowel clusters. The mid vowels *e and *o are required to account for Ryukyuan correspondences. In Old Japanese, they were raised to i and u respectively, except in word-final position. They have also left some traces in eastern Old Japanese dialects. Some authors also propose a high central vowel *ɨ to account for alternations in Old Japanese, but there is no evidence for it in Ryukyuan or Eastern Old Japanese.
The Japanese pitch accent is usually not recorded in the Old Japanese script. The oldest description of the accent, in the 12th-century dictionary Ruiju Myōgishō, defines accent classes which generally account for correspondences between modern mainland Japanese dialects. However, Ryukyuan languages share a set of accent classes that cut across these. For example, for two-syllable words, the Ruiju Myōgishō defines five accent classes, which are reflected in different ways in the three major accent systems of mainland Japanese, here represented by Kyoto, Tokyo and Kagoshima. In each case the pattern of high and low pitches is shown across the two syllables and a following neutral particle. Ryukyuan languages, here represented by Kametsu, show a three-way division that partially cuts across the five mainland classes.
| Class | Kyoto | Tokyo | Kagoshima | Kametsu | |
|---|---|---|---|---|---|
| 2.1 | HH-H | LH-H | LH-L | LH-H | |
| 2.2 | HL-L | LH-L | |||
| 2.3 | LL-H | (a) HL-L |
(b) LH-L | ||
| 2.4 | LL-H | HL-L | |||
| 2.5 | LH-L | ||||
In some Ryukyuan dialects, including Shuri, subclass (a) is marked by a long vowel in the first syllable instead of a distinct pitch pattern, leading Hattori to suggest that the original distinction was one vowel length.