The benchmark Nikkei 225 Stock Average closed down 469.80 points, or 3.22 per cent, at 14,142.65, while the broader-based Topix index dropped 40.01 points, or 3.35 per cent, to end the day at 1,154.07.
A stronger yen increases the price of Japanese-made goods overseas and erodes repatriated earnings.
The drop came two trading days after the exchanges lost 7.32 per cent and 6.87 per cent, respectively, on Thursday, after an index of purchasing managers' business confidence in China showed sentiment unexpectedly dropping.
Stocks jumped by around 2.5 per cent during trading Friday, before settling to close with the Nikkei recouping just 0.89 per cent from the previous day's rout, and the Topix just 0.48 per cent.//DPA