The January figure was the first time the monthly deficit went over the 2 trillion yen mark. It was also 70.8 percent higher than the deficit of 1.63 trillion yen in same month of last year, the Finance Ministry said.
The January deficit came on top of December's deficit of $12.7 billion, which pushed the world's third largest economy's deficit for all of 2013 to record highs of 11.45 trillion yen or $112.07 billion.
The January numbers were the 19th straight month when Japan's export-dependent economy reported a trade deficit.
January imports, driven mostly by energy costs, jumped 25 percent year-on-year, to a record 8.04 trillion yen. Crude oil imports in January jumped over 28 percent, while liquefied natural gas imports rose 21.4 percent.
January exports rose 9.5 percent year-on-year to 5.25 trillion yen.
Prime Minister Shinzo Abe's government and the Bank of Japan have introduced a number of stimulus measures including sharply raising the money supply and doubling the inflation target to 2 percent to lift the economy out of 15 years of crippling deflation.
The measures have brought down the value of the yen needed to boost exports. The yen has depreciated more than 20 percent in the past year.
However, a lower yen also has driven up imports costs as Japan has had to increase its energy imports with the closure of its nuclear power plants following the earthquake-triggered March 2011 nuclear disaster at the Fukushima-Daiichi plant.
January exports to China, Japan's largest trading partner, rose 13.1 percent to 862.6 billion yen, but imports from China jumped 34.4 percent to 1.91 trillion yen.
January exports to Asian nations, excluding China, were up 5.8 percent to 2.70 trillion yen, but imports soared 27.2 percent to 3.67 trillion yen.
January exports to the United States increased 21.9 percent to 1.02 trillion yen, and imports rose 25.9 percent to 656.4 billion yen. Exports to the European Union were up 20.2 percent to 611.1 billion yen, and imports totaled 699.7 billion yen.
Economists, commenting on the deficits, told the Wall Street Journal that the trend of Japan's large manufacturers moving production operations overseas has affected the benefits of a lower yen. The overseas move is prompted by the need to be closer to the customer base and to reduce the risks of currency fluctuations, they said.
Another concern is that Japan's sales tax rate is scheduled to go up in April to 8 percent from the current 5 percent, which could affect domestic demand.