The 4.1 trillion yen (USD 35.8 billion) surplus compared with a 2.8 trillion yen deficit in 2015. Exports fell 7.4 per cent from a year earlier while imports dropped 16 per cent.
Japan's trade surplus with the US fell nearly 5 per cent.
Japan's trade balance slipped into deficits after the 2011 earthquake and tsunami triggered meltdowns at the Fukushima Dai-Ichi nuclear plant and the country's reactors were shut down for safety checks.
To compensate, resource-poor Japan ramped up imports of oil, gas and coal for its conventional power generators. In 2016, imports from the Middle East, Japan's main source of crude oil, dropped by nearly a third from the year before.
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