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Government figures showed a 35.1 percent on-year rise to a 1.29 trillion yen ($12.6 billion) deficit, the worst result for November and the 17th straight month of shortfall -- the longest stretch since comparable data began more than three decades ago.
Japan's energy imports surged after the 2011 Fukushima crisis forced the shutdown of the country's nuclear reactors, which once supplied a third of the nation's power.
A sharp decline in the yen, which is good for exporters' profitability, has also forced up the cost of importing pricey fossil-fuels to plug the country's energy gap.
The yen has been under pressure since Japanese Prime Minister Shinzo Abe, who took office late last year, launched a policy blitz that meshed government spending with a central bank monetary easing plan unveiled in April.
The policy drive, dubbed Abenomics, is aimed at rebooting the world's third-largest economy, which has suffered from growth-sapping deflation for years.
Wednesday's trade figures come on the back of slowing GDP growth after a sizzling expansion that saw Japan outpace other G7 nations in the first half of the year.
Japan's third-quarter economic growth came in at a final reading of 0.3 percent, down from an initial figure of 0.5 percent -- and a sharp slowdown from 0.9 percent growth in the previous quarter.
But firms appear to be taking the slowdown in their stride. On Monday, a Bank of Japan survey that polls more than 10,000 companies showed business confidence has soared to a six-year high.
Part of the reason is the sharp weakening of the yen over the past year, which has seen Japanese exporters such as Sony and Toyota booking rosy profits as the cheaper unit made them more competitive overseas while inflating repatriated earnings.
That benefit showed up in the trade data as exports last month rose 18.4 percent to 5.90 trillion yen, backed by robust shipments of automobiles.
Imports soared 21.1 percent to 7.19 trillion yen, owing to Japans' hefty bills for oil and gas purchases.
Exports expanded in most major regions, with US-bound shipments up 21.2 percent to 1.13 trillion yen while those to the European Union rose 19.4 percent to 599.4 billion yen.
Goods shipped to Japan's biggest trading partner China surged 33.1 percent to 1.14 trillion yen, as the impact of a consumer boycott on Japanese brands fades.
The boycott came after a Tokyo-Beijing territorial dispute over islands in the East China Sea set off protests in China and soured already testy relations between the Asian giants.
As the conservative prime minister nears his one-year anniversary, there is rising speculation that the central bank will expand its easing programme -- which injects vast sums into the financial system -- as growth slows and consumers prepare for a sales tax hike that critics fear will derail a budding recovery.
Tokyo has approved a spending package worth almost $54 billion to offset the tax hike -- to 8.0 percent from 5.0 percent -- seen as crucial to bring down Japan's huge national debt.
Analysts have warned that Abe's bold pro-growth programme is not enough on its own without promised economic reforms.
A proposed shake-up, including loosening labour laws and signing free trade deals, is seen as key to ushering in lasting change.
