Analysts worry that a China-led global slowdown could drag down the Japanese economy, keeping Tokyo under pressure to deploy fresh monetary and fiscal stimulus in the coming months.
"China-bound exports fell for a second straight month in terms of value and volume, that weighed on exports," a finance ministry official said. "We must pay the utmost attention to China."
Exports to China fell 3.5 percent in September from a year earlier, down for a second straight month and weighed by falling shipments of light oil and car parts.
Shipments to Asia - which account for about a half of Japan's overall exports - fell 0.9 percent in the year to September. That was the first decline in seven months.
Exports to the United States, a major buyer of Japanese products, rose 10.4 percent in September, led by brisk shipments of cars. That followed a 11.1 percent annual gain in August.
Reflecting ongoing falls in oil prices, imports fell 11.1 percent in the year to September, largely in line with economists' estimates.
The trade balance was a deficit of 114.5 billion yen ($955 million), versus an 84.4 billion yen surplus seen by economists, marking six straight months of deficits.