Investors ignored government data that showed Japan's core machinery orders rose 13.0 percent in March from the previous month.
Meanwhile, in a rare and explicit statement, U.S. Treasury Secretary Scott Bessent and Japanese Finance Minister Katsunobu Kato agreed on Wednesday that the dollar-yen exchange rate currently reflects fundamentals.
The Nikkei average fell 0.84 percent to 36,985.87, hitting a two-week low. The broader Topix index settled 0.58 percent lower at 2,717.09.
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