The Nikkei 225 index has closed at 12,853.97, down 249.97 points in volatile trade on profit-taking following yesterday's sharp gains.
Dealers also blame the fall on increased caution over the prospects for an early resolution to bad-loan problems.
The dollar was at 123.66 yen, up from 123.40 in late New York trading, and at 0.8956 against the euro, compared with 0.8955 in New York.
Dealers say the dollar rallied against the yen in mid-afternoon trading on concerns that relations between the US and Russia may deteriorate sharply following reports that Washington is expelling 50 Russian diplomats following the arrest of an FBI agent accused of spying for Moscow.
In Tokyo trading, government bond yields were higher, with bond no 228 yielding 1.050% and bond no 229 yielding 1.070%.
The US 30-year government bond was trading at 101-12/32, yielding 5.285%, down from 101-14/32, yielding 5.270%, in late New York trade.