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The fall was driven by declines in both the construction and mining industries, it said.
Construction activity dropped by 8.3%, leading to a reduction in the demand of materials such as iron ore, steel profiles and steel pipes, Inegi said.
Mining output went down by 1.2%.
Manufacturing output and utilities production, on the other hand, increased by 1.2% and 1%, respectively.
The country’s industrial output has been falling over the past few months, according to Inegi figures.
However, in August when industrial output was down 0.7% year-on-year, crude steel production was up 10% to 1.6 million tonnes, according to preliminary figures from Latin America's steel association, Alacero.
Mexico's steel association, Canacero, has not released figures for August.
Mexico’s industrial output fell by 1.6% year-on-year in September, mainly due to a reduction in mining and construction activity, according the country’s statistical agency, Inegi.