The declining yen helped boost exports, but also drove up cost of imports, especially of energy, on rising demand, data released Wednesday by the Finance Ministry showed.
The November figure was the 17th straight month when Japan, the world's third largest economy, has reported a deficit.
November exports rose 18.4 percent year-on-year to 5.9 trillion yen. However imports during the month soared 21.1 percent 7.19 trillion yen.
Japan's energy imports have jumped to make up for the sharp decline in domestic nuclear power generation with the shutdown of Japanese reactors following the nuclear disaster set off by the March, 11, 2011, earthquake and tsunami.
In the first 11 months of this year, Japan's trade deficit has exceeded 10 trillion yen, up from 6.9 trillion in the same period of last year, Kyodo News reported.