The Nikkei index started the day strong and hit a new high of 31,352.53 points, a level last recorded in August 1990.
But it pared gains after the lunch break, with more investors selling shares to take profits.
The declines followed quickly, pushing the index down 0.83%, before ending the session down 0.42% at 30,957.77 points.
Shares of Toyota Motor plunged 4.77% in the final minutes of trading, becoming the biggest loser in the Nikkei index.
The broader Topix index also fell, by 0.66%, to 2,161.49 points.
Chipmaking equipment giant Tokyo Electron fell 2.57%, while Advantest fell 1.67%.
But there were more resilient chip-related stocks, such as Trend Micro and Renesas Electronics, which were among the biggest gainers on the Nikkei index, rising 2.94 and 2.21% respectively.
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