The benchmark Nikkei 225 slid 0.31 percent, or 63.14 points, to close at 20,267.05 despite the weaker yen as most automakers, financials and trading houses pulled back.
The index slipped 0.12 percent to close at 5,664.3 with the information technology and telecommunication services sub-indexes leading losses.
On the mainland, the Shanghai Composite inched higher by 0.06 percent to close at 3,345.4633 and the Shenzhen Composite advanced 0.776 percent to close at 1,979.2795.
The dollar also clawed back gains against the Japanese currency to fetch 112.73 yen.
The Dow Jones industrial average slipped 0.05 percent, or 11.77 points, to close at 22,284.32, but the S&P 500 and tech-heavy Nasdaq finished slightly higher.