The virus that causes COVID-19 was present in samples from Milan and Turin on December 18 and in Bologna on January 29.
Italy's first known native case was discovered mid-February.
The findings could help scientists understand how the virus began spreading in Italy, Ms La Rosa said.
The results feed into an effort by scientists around the world to trace the virus's family tree.
Lazio, the region including the capital Rome, topped the number of cases, exceeding Lombardy, the original epicentre of the epidemic in the country.More news: AMC Entertainment to reopen 450 United States theaters on July 15
A genetic study of samples from more than 7,500 people infected with COVID-19 indicated that the new coronavirus spread quickly around the world after it emerged in China sometime between October and December a year ago.
On February 21 the government ordered Codogno shuttered, followed by nine other towns across Lombardy and Veneto.
40 samples from October 2019 to February 2020 and 24 samples from September 2018 through June 2019 serving as a control group to rule out the possibility of the presence of the virus have been analyzed, according to researchers.
Samples taken in October and November 2019 tested negative.
Italy has been one of the countries worst hit by the coronavirus pandemic, but since May has seen a slowdown in the contagions and death rates. The results are consistent with similar tests carried out on waste water in Barcelona and with clinical tests on patients hospitalized in France, which showed biological traces of the virus as early as last December.More news: SEC Urging Mississippi To Change State Flag, Threatens To Pull Title Games
The new ISS study "may contribute to shedding light on the first phase of the virus's circulation in Italy", La Rosa said.
Luca Lucentini, who leads the Italian health institute's department for Quality of Water and Health, said the Italian discovery does not mean "the main transmission chains that led to the development of the epidemic in [Italy] originated from these first cases".
The ISS said it had urged the health ministry to coordinate the collection of samples regularly in sewers and at the entrance to purification plants "as a tool to detect and monitor the circulation of the virus in different territories at an early stage".
The institute says it aims to begin a pilot project monitoring waste water at tourist resorts in July with a view to setting up a nationwide waste water monitoring network later this year.More news: Read Senate Republicans' Proposed Police Reform Legislation