Overseas shipments fell 4.5% in November from a year earlier, Ministry of Finance data showed.
The strength of the Japanese yen as well as the ongoing European debt crisis have weighed on external demand.
Meanwhile the Bank of Japan has decided to keep its key interest rate on hold at between zero and 0.1%.
Japan’s economy recovered from a recession that was sparked by the devastating tsunami and earthquake in March.
However in recent months the boost from recovering supply chains and restored production facilities has started to diminish.
Japanese exports came in at 5.2 trillion yen ($66.8bn; £42.6bn) in November, falling for the second straight month.
Imports rose 11.4% to 5.88tn yen, the ministry said. That lead to an expansion in the trade balance deficit to 684.7bn yen.
The other challenge that the global economic uncertainty brings is that investors are turning to the yen as a safer investment.
That has boosted the currency making Japanese exports more expensive overseas.
The problem is such a concern that the government has intervened in the currency markets to try and reduce the impact.
On Tuesday authorities said they will expand the funds available for more currency interventions in the future.