The trade surplus in September fell to 957.0 billion yen ($8.31 billion), down 21.1 percent from a year earlier. Forecasts had centred on a surplus of 850 billion yen, which would have represented a fall of 30 percent.
Economists said that while growth in exports was overshadowed by the surge in import costs, overseas demand continued to bolster Japanese business activity.
"In volume terms, exports were up for the second straight month, and this is a good sign for the economy," said Seiji Adachi, senior economist at Deutsche Securities. "Slow growth in exports is becoming less of a risk factor for the economy."
Exports rose 8.8 percent from a year earlier to 5.9253 trillion yen, led by cars and steel. On a volume basis, exports rose 1.2 percent.
Imports rose 17.4 percent to 4.9683 trillion yen, with crude oil imports contributing 8.5 percentage points, or about half, of the overall rise in imports, the Ministry of Finance said on Wednesday.
The Japan Crude Cocktail price, or the average price for customs-cleared crude oil imports, was a record $59.34 a barrel for September, up from $55.50 a barrel in August. On a seasonally adjusted basis, the trade surplus was 556.5 billion yen, down 8.9 percent from August. Exports to China, which rose 14.4 percent from a year earlier, have picked up again after weakening from late last year as China's economy shows little sign of slowing down.