Japan logged a deficit of 1.45 trillion yen ($14 billion) against the year-before shortfall of 356.9 billion yen, the finance ministry said.
Exports rose 1.8 per cent to 6.38 trillion yen, thanks to higher shipments of cars and processed fuel products.
But imports grew a much faster 18.1 per cent to 7.83 trillion yen due to higher imports of crude oil and liquefied natural gas.
Energy imports surged after the 2011 Fukushima crisis forced the shutdown of Japan'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.
The yen was an average 8.7 per cent cheaper against the dollar in March compared with the year-before level, according to customs data.
Japanese domestic demand for gasoline and other products also picked up in March ahead of the April 1 sales tax hike from 5.0 per cent to 8.0 per cent.