The 225-issue Nikkei Stock Average finished down 119.79 points, or 0.40 percent, from Tuesday at 29,688.33.
The broader Topix index of all First Section issues on the Tokyo Stock Exchange ended 12.49 points, or 0.61 percent, lower at 2,038.34.
Declining issues were led by air transportation, service, and farm and fishery issues.
Tokyo stock market moved in the negative territory most of the time after rising for four consecutive days through Tuesday when the benchmark Nikkei index closed at a seven-week high, as the U.S. currency remained strong against the yen throughout the day, which made investors worried about materials costs to grow higher.
"Although the weaker yen is good for some exporters, it served as an excuse for investors to lock in gains today on concerns over rising materials costs," said Yutaka Miura, senior technical analyst at Mizuho Securities Co.
Worries over increasing fuel costs dragged down the airline issues, with Japan Airlines dropping 69 yen (0.6 U.S. dollar), or 2.8 percent, to 2,435 yen (21.2 dollar) and ANA Holdings sliding 59 yen (0.5 dollar), or 2.1 percent, to 2,716 yen (23.6 dollar).
Going against the downward trend, oil refiner Idemitsu Kosan gained 35 yen (0.3 dollar), or 1.2 percent, to 3,070 yen (26.7 dollar), and oil explorer Inpex increased 19 yen (0.2 dollar), or 1.9 percent, to 1,004 yen (8.7 dollar) after the industry ministry said Tuesday it is focusing on subsidizing oil companies to curb the growth in gasoline prices.
On the First Section, decliners outnumbered advancers 1,706 to 410, while 67 finished unchanged.
Trading volume on the main section declined to 1,173.39 million shares from Tuesday's 1,190.59 million shares.
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