The Nikkei 225 index at the Tokyo Stock Exchange, which soared 1.24 percent on Wednesday, lost 71.40 points to stand at 8,488.71.
The Topix index of all first-section issues slipped 0.90 percent, or 6.71 points, to 736.28.
The euro fetched $1.2930 and 99.21 yen in Tokyo afternoon trade, down from $1.2941 and 99.28 yen in New York late Wednesday. The dollar was flat at 76.72 yen.
Profit-taking was setting in after the previous day's strong gains, said Daiwa Securities senior market analyst Yumi Nishimura.
"There are hopes for bullish US economic indicators, including ADP employment data later today, which will likely furnish the Nikkei with some sentimental support," she told Dow Jones Newswires.
Payrolls firm ADP is to release private-sector hiring data for December ahead of the closely watched government jobs report Friday.
Honda shares rose 0.40 percent at 2,453 yen following Wednesday's sharp run-up, illustrating some follow-through buying amid broader market weakness. Toyota was unchanged at 2,644 yen.
The shares were seen benefiting from solid December sales announced by all three Detroit automakers.
US blue chips pushed higher Wednesday but the broader market was virtually flat amid hesitant trade.
The Dow Jones Industrial Average finished up 0.17 percent at 12,418.42 while the broader S&P 500 was flat, adding just 0.02 percent to 1,277.30.