Bear in mind that there were two main 'Air Forces' used by Japan in WW2 - Navy (IJN) and Army (IJA). They often used different colour sets and I believe that IJA aircraft used brown as one of their camouflage colours (either as a single block colour as per below) or possibly patches depending on local conditions. Particularly later in the war I think standardisation of markings was of a low priority combined with shortages of materials - a squadron on some island chain in the middle of nowhere would likely use what they had.
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This chap has an almost unhealthy level of research available on WW2 Japanese aircraft colours - well worth a trawl through the site.
Aviation of Japan 日本の航空史
Japanese aircraft are also probably the least well-referenced in terms of photographic evidence - Soviet stuff of similar vintage being similarly vague. Absence of evidence is not evidence of absence seems to be a good rule of thumb in these cases....