The benchmark Nikkei 225 Stock Average lost 1,143.28 points, or 7.32 per cent, to end at 14,483.98, while the broader-based Topix index was down 87.69 points, or 6.87 per cent, at 1,188.34.
An unexpectedly weak index of purchasing managers' sentiment in China published earlier by the bank HSBC Holdings Plc was blamed by some analysts for the slump in confidence in export-dependent Japan.
The preliminary data showed an index reading of 49.6, lower than predictions by analysts, and below the 50 mark for the first time in seven months.
Economists polled by financial news agency Bloomberg had predicted the index would hold steady at April's figure of 50.4.
Falling below 50 indicates overall contraction, and raised fears of a second consecutive quarter of slowing growth in the world's second-largest economy.
Japanese stocks were also hurt by a strengthening in the yen, which makes exports more expensive overseas and erodes repatriated earnings.