The deficit for the month rose to 932 billion yen, up 64 percent from a year ago, as imports rose 16.5 percent, Japan's Ministry of Finance said.
The yen has fallen nearly 25 percent against the U.S. dollar since November with Prime Minister Shinzo Abe's economy stimulus plan - including massive central bank monetary easing - making exports cheaper but the growth in exports has not been sufficient enough to offset the higher import bill.
The data showed that exports rose 11.5 percent in September, from a year earlier.
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