By Agence France-Presse
The world's third-largest economy registered a trade balance deficit of 943.4 billion yen ($887 million) in January, the first since May last year, the finance ministry said.
The market had expected a deficit of 1.02 trillion yen.
Exports rose 12.2 percent to 6.086 trillion yen but imports also rose 7.9 percent to 7.029 trillion yen.
The yen was on average 3.4 percent higher against the dollar compared to the same month a year earlier.
Still, the costs of imports in crude oil, medical products and liquified natural gas increased as the volume of trade in such items grew, the ministry said.
Japan's often politically sensitive trade surplus with the United States shrank 12.3 percent on increased imports of liquified natural gas, organic chemicals and medical products.
For decades into the 1990s, the two countries battled over their trade flows, but the balance has become less of a hot-button issue under recent US administrations, with China's trade surplus a greater concern for Washington.