The Nikkei average dipped 0.26 percent to 39,981.06 while the broader Topix index settled 0.59 percent lower at 2,770.
Fast Retailing, Uniqlo's parent company, dropped half a percent ahead of its first-quarter results due on Thursday.
Chip stocks bounced back in an otherwise subdued market, with Advantest rallying 3.4 percent and Tokyo Electron gaining 1.6 percent.
Japan's consumer sentiment decreased unexpectedly at the end of the year, survey data from the Cabinet Office showed on Wednesday. The seasonally adjusted consumer confidence index weakened to 36.2 in December from 36.4 in November.
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