The IHS Markit Purchasing Managers Index (PMI) fell to 48.4 in June from 49.7 in May, the lowest reading since March and slipping further below the 50 mark that separates growth from contraction.
A Reuters survey of 11 analyst had pointed to 48.8.
IHS Markit said its sub-index for new orders at manufacturers fell in June to 47.4 from 49.6 in May.
The euro zone's third-largest economy eked out growth of 0.1% in the first quarter from the previous three months, emerging from a shallow recession during the second half of last year.
National statistics bureau ISTAT has warned that the second quarter could show the economy contracting again.
The government of the anti-establishment 5-Star Movement and the right-wing League forecasts full-year growth of just 0.2%, leaving Italy in its customary position among the euro zone's most sluggish economies.