The shortfall of 11.47 trillion yen marked the biggest deficit since comparable data started in 1979, according to the finance ministry, with the December deficit alone doubling from a year earlier.
Japanese energy imports surged after the 2011 Fukushima crisis forced the shutdown of nuclear reactors that once supplied a third of the nation's power.
A sharp decline in the yen, which is good for exporters' profitability, also forced up the cost of importing pricey fossil-fuels to plug the country's energy gap.
Exports in 2013 rose 9.5 percent to 69.79 trillion yen, their first increase in three years.
The increase pointed to recovering demand in China after a Tokyo-Beijing diplomatic row sent trade tumbling, as well as improved demand in the key US and European markets.
However, imports outpaced the rise in shipments abroad, jumping 15.0 percent to their highest-ever level of 81.26 trillion yen.