Japan's benchmark Nikkei stock index, the 225-issue Nikkei Stock Average, ended down 85.57 points, or 0.22 percent, from Monday to close the day at 38,837.46.
The broader Topix index, meanwhile, finished 10.59 points, or 0.38 percent, lower at 2,787.48.
Market watchers here noted a market trend of selling on recovery and profit taking as the Nikkei approached the 39,000 psychological milestone on the day, adding that the yen's appreciation also weighed on the market.
Stock prices of major Japanese automakers including Toyota and Honda saw significant losses, after five major vehicle makers admitted falsifying certification tests for their products.
On the top-tier Prime Market, decliners were led by mining, insurance, and oil and coal product issues.
Issues that fell slightly outpaced those that advanced by 799 to 794, while 54 ended the day unchanged.
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