This is a great matter of dispute and we lack yet conclusive evidence.
There are several similarities between Austronesian (especially certain branches on Taiwan) and Japonic languages. Several linguists support a genealogical relation, but others suggest the similarities are because of language contact during the proto-state of Japonic in southern or eastern China.
It is generally agreed that proto-Japonic originated somewhere in southern or eastern China and stood in contact with the local languages before they migrated into the Korean Peninsular in 1500BC and create the Mumun/Yayoi culture (see Peninsular Japonic).
Several studies support a link between Japonic languages and wet-rice cultivation in Northeast Asia. There is also evidence that vocabulary about rice cultivation was borrowed from Peninsular Japonic into Koreanic languages
Holmer 2010 notes that the evidence for a genealogical relation between Japanese and Austronesian should not be ignored. He further states that the evidence is stronger than evidence for other proposals such as Korean or Altaic.
Yoshizu Itabashi (2011) shows that similarities in morphology, phonology and basic vocabulary point towards "a strong genealogical connection between Japanese and Austronesian". He further states that:
Finally, it is worth noting that Japanese and Austronesian have a common variety of prefixes, which are treated as morphology and syntax as opposed to phonology, and which are normally not borrowed, as well as the regular phonological correspondences and much common basic vocabulary.
Elmer 2019 summarized that the most likely homeland of proto-Japonic was somewhere in southern or eastern China. A genealogical relation to local languages such as Austronesian is possible, but lacks yet conclusive evidence.
It was found that Japonic must have also been in long-term contact with Kra-Dai languages, as they share basic vocabulary which is seldom borrowed.
The contact zones in southern China and Manchuria:
Some examples of proposed cognates:
A Bayesian analysis supports the homeland in southern China. Analysed vocabulary correspond to an wet-rice related agricultural origin.
Conclusion:
There is evidence for a genealogical relation between Japonic and Austronesian, but we yet lack conclusive evidence. The mainland Austronesian branches may have been more similar to Japonic or are in fact ancestral to proto-Japonic.
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