The agency said that 84 cases of the new strain had been identified on Saturday, up from 55 on Friday.
Thirty-three cases were found in the Lombardy region in northern Italy and a further 20 in the southern region of Campania.
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Test sequencing is more limited in Italy however than in some countries, such as the UK.
The spread was “widely expected, in line with what we have seen in other countries, and we will probably see an increase in cases in coming days,” ISS president Silvio Brusaferro said, Reuters reported.
This came as the World Health Organisation said that Omicron was spreading rapidly even in countries with high levels of population immunity.
EU chief Ursula von der Leyen has warned that the Omicron variant could be dominant in Europe by mid-January.
As of December 17th, around 85 percent of Italy’s total population was fully vaccinated against Covid-19, according to Statista, rising to almost 94 percent for the over-80 age group.
On Saturday, Italy reported 123 coronavirus-related deaths and 28,064 new infections, the health ministry said.