Istat, the national statistics agency, said on Monday that the decline affected all industrial sectors.
Analysts had forecast a 0.2 percent fall from August and a 0.7 percent fall from September last year.
The drop will further stall recovery in the eurozone’s third-largest economy, piling more pressure on Italy’s Prime Minister Matteo Renzi to quickly implement measures to revive growth.
A European Commission report last week forecast that the Italian economy would grow at 0.6 percent next year, spurring a “fragile recovery”.
Italy's jobless rate also rose to 12.6 percent in September, from 12.5 percent in August.