The new figures leave China with a trade surplus of 376.2 billion yuan ($59.4 billion).
The steep fall in imports compares with a fall of 14.3% in August and continues to reflect lower commodity prices globally.
China recently revised down its 2014 economic growth from 7.4% to 7.3%.
The revision marks its weakest growth for almost 25 years. After decades of double-digit growth, the government is expecting to see growth of about 7% in 2015.
China is attempting to shift from an export-led economy to a consumer-led one.
Exports in September held up better than expected, after some had forecast a fall of as much as 7%.
However, the significant fall in imports means domestic demand is not as strong as the government would have hoped.
China’s official trade numbers in US dollar denominated terms were reported shortly after the yuan-denominated numbers.
They showed exports fell a less-than-expected 3.7% in September, while imports slumped 20.4% from a year earlier. The numbers leave the country with a surplus of $60.34 billion for the month – which the government said was higher than expected.
Currency conversion factors based on US dollar and Chinese yuan movements over the last year mean some official numbers from the mainland are now reported in both currencies.
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