Japan's benchmark Nikkei stock index, the 225-issue Nikkei Stock Average, ended down 11.58 points, or 0.03 percent, from Wednesday to close the day at 35,466.17.
The broader Topix index, meanwhile, finished 4.29 points, or 0.17 percent, lower at 2,492.09.
Market watchers here pointed out that profit-taking selling dominated Thursday's market in Tokyo as caution stems from short-term overheating concerns amid rapid surges in Nikkei since the beginning of the year, while many investors took a wait-and-see attitude ahead of the Bank of Japan's policy meeting next week.
Meanwhile, as the weak yen raised prospects of higher profits among exporters, transport equipment and other export stocks were bought, with Toyota updating its substantial all-time high.
On the top-tier Prime Market, decliners were led by land transportation, insurance and electric power and gas issues.
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