It was the third straight month of deficits for export-dependent Japan, which has the world's third-largest economy after the United States and China.
In releasing the September numbers, Japan's Finance Ministry said exports during the month totaled 5,359.75 billion yen, or $67.6 billion, down 10.3 percent from the same month of last year. Imports rose 4.1 percent to 5,918 billion yen, or $74.6 billion.
Deficits in the first half of the current fiscal year beginning April 1 soared to $40.6 billion, up 90.1 percent from a year earlier and the highest since the Finance Ministry began recording them in 1979, Kyodo News reported.
The September numbers raised concerns the dispute with China has begun to impact bilateral economic ties, the Japanese news agency said.
In addition to the global slowdown that has hit its exports, Japan is also embroiled in a growing territorial dispute with China, its largest trading partner. The dispute involves a group of Japan-controlled uninhabited islands in the East China Sea, which China also claims.
The territorial issue worsened after the Japanese government last month announced the purchase of the islands, triggering violent protests in China and damaging bilateral trade of about $340 billion annually.
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