
The benchmark Nikkei 225 index lost 0.51 percent, or 98.80 points, to 19,287.01 in the first few minutes of trade, while the broader Topix index was down 0.59 percent, or 9.32 points, at 1,581.39.
"No one knows if the issues around North Korea will finally settle into dialogue or lead to military actions," Mitsushige Akino from Ichiyoshi Asset Management told Bloomberg News.
Jittery traders are profit-taking at this time of "intensifying tensions," he added.
Concerns about North Korea weighed on share prices around the world with US stocks falling sharply in their first day of trading after a long holiday weekend.
The blue-chip Dow Industrial Average closed down 1.1 percent at 21,753.31.
The yen traded stronger against the benchmark dollar.
In early Asian trade Wednesday, the dollar bought 108.57 yen, down from 108.79 yen in New York late Tuesday.
Turning to individual Japanese stocks, Toshiba shares soared more than four percent after reports that US partner Western Digital would offer a fresh proposal to purchase its memory chip business.
The stronger yen also weighed on global exporting companies such as Japan's auto giants, with Toyota down 1.17 percent at 6,146 yen, Honda lower by 0.68 percent at 3,036 yen and Nissan off 1.00 percent at 1,081.5 yen.
Panasonic was down 0.58 percent at 1,440 yen, while market heavyweight and Uniqlo casual clothing firm Fast Retailing was down 1.53 percent at 30,870 yen.