Analysts said that the Japanese market's rise had steadied while the yen's fall had lost momentum as investors grew wary of taking large positions until there was clarity on Bank of Japan's next governor.
Investor sentiment soured on Tuesday after Finance Minister Taro Aso told a news conference he was not considering foreign bond purchases for monetary stimulation.
His comments sent the dollar as low as to 93.56 yen, with exporters losing ground as investors assessed how far a new BOJ governor could practically expand monetary stimulus.
"The appointment of the new governor will somewhat determine the direction of the Nikkei for the short term," said Takuya Takahashi, an analyst at Daiwa Securities.
The Nikkei dropped 0.3 percent to 11,372.34, after jumping 2.1 percent on Monday to near a 4-year high struck on February 6.
Economy Minister Akira Amari said on Tuesday the government will decide on the Bank of Japan's new governor and two deputies after Prime Minister Abe returns from a trip to the United States over February 21-24.
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Daiwa's Takahashi added that in the longer term, the appointment should have a limited impact on the market, with most investors convinced that whoever takes the job will have to implement an easy monetary policy under Abe-led government.
Index heavyweight Fanuc weighed on the benchmark after the Japan Machine Tool Builders' Association said machine tool orders to China had dropped 65 percent in January compared to the previous year.
Robotics builder Fanuc dropped 4.1 percent, taking 24.7 points off the benchmark.
Carmakers weakened, with Toyota Motor Corp falling 0.9 percent, Nissan Motor Co dropping 1.1 percent and Mazda Motor Corp shedding 0.7 percent.
The broader Topix added 0.1 percent to 963.61 as stellar profits for tyre maker Bridgestone Corp helped the rubber products sub-index jump 8.0 percent as the best-performing sector.
Bridgestone soared 10 percent after the tyre maker announced a 50 percent increase in its operating profit for the year ended December 31, and overshot analysts' estimates with its current year profit forecast.
The stock was the third-most-traded stock by turnover on the main board.
On the main board, volume was thin, with 2.69 billion shares changing hands, compared with last week's daily average volume of 4.03 billion shares.
Abe and U.S. President Barack Obama are expected to discuss Japan's possible entry into regional free trade talks with the United States later this week.
""We would expect a positive impact on share prices if the Japanese government clarifies its views on participation in the TPP (Trans-Pacific Partnership) at the US-Japan summit, and starts to roll out growth strategy initiatives seriously," said Hiromichi Tamura, chief strategist at Nomura Securities.