The 225-issue Nikkei Stock Average dropped 199.47 points, or 0.72 percent, from Tuesday to close the day at 27,686.40.
The broader Topix index, meanwhile, lost 1.91 points, or 0.10 percent, to finish at 1,948.31.
Dealers here said that technology-related issues came under pressure following the U.S. tech-heavy Nasdaq ending down for a second straight day overnight.
Crude oil price dropping overnight sent energy shares lower, they added, with investors seeking out defensive shares that are less susceptible to outside factors, like railway and utility stocks.
"With high-tech shares down, investors' money flowed into stocks that are less susceptible to outside factors," Toshikazu Horiuchi, equity strategist at IwaiCosmo Securities Co., was quoted as saying.
By the close of play, air transportation, electric power and gas, and bank issues comprised notable gainers, while mining, electric appliance and machinery issues led those that declined the most.
Among chip issues following their U.S. peers lower, chipmaking equipment maker Tokyo Electron dropped 3.8 percent, while semiconductor silicon wafer maker Shin-Etsu Chemical lost 1.6 percent.
Energy shares losing ground on an overnight drop in crude oil prices included oil exploration giant Inpex losing 1.6 percent.
But defensive issues helped trim losses, with East Japan Railway climbing 1.8 percent, while Kansai Electric Power jumped 2.8 percent.
Notable winners included cosmetics maker Shiseido, who added 2.1 percent and department store operator Isetan Mitsukoshi Holdings, who gained 3.5 percent on hopes for increased patronage.
Game and console maker Nintendo reversed earlier losses to end 0.3 percent higher, following reports Microsoft's gaming division chief had said a 10-year commitment to bring the "Call of Duty game title to its platforms had begun."
Issues that rose outpaced those that fell by 1,049 to 686, while 101 ended the day unchanged.
On the Prime Market on Wednesday, 1,045.70 million shares changed hands, rising from Tuesday's volume of 1,016.22 million shares.
The turnover on the third trading day of the week came to 2,636.18 billion yen (19.15 billion U.S. dollars).
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