The deficit for the month rose to 932bn yen ($9.5bn; £5.8bn), up 64% from a year ago, as imports rose 16.5%.
A series of aggressive measures aimed at reviving Japan’s economy has resulted in the yen falling nearly 25% against the US dollar since November.
While that has helped Japan’s exports by making them cheaper, it has also made imports more expensive.
However, the growth in exports has not been sufficient enough to offset the higher import bill.
Data released by the Ministry of Finance showed that exports rose 11.5% in September, from a year earlier.
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