One opposition MP expressed fears that the move at the height of the tourist season could alarm visitors to the city.
But Gianni Alemanno, the mayor of Rome, said no soldier would patrol in the historic centre where most tourists are concentrated.
Roberto Maroni, the interior minister, told reporters in Rome last week that he wanted to "give the public a better perception of security".
Paola Zabaglia, a commuter at Anangnina underground station, in a suburb of southeast Rome, welcomed the troop deployment.
"It is surely useful and people feel safer. It is important that they don't exceed in their duties but I am sure that it will be so," she said.
However, Ferruccio Paglia was not so sure saying: "I believe there are other ways to guarantee legality."
The measure, proposed by the goverment of Silvio Berlusconi, the prime minister, was approved by parliament last month and will remain in effect for six months.
Maroni gave details of the operation at Tuesday's news conference.
"The forces deployed amount to 3,000 units from the army, the navy, the air force, and Carabinieri with military duties," Maroni said.
"Of these, 2,000 are destined to the surveillance of sensitive sites and targets. In particular, 1,000 are destined to exterior surveillance of the immigration centres or CIE (centres for identification and expulsion), formerly known as CPT (centres for temporary stay)."
In Milan, troops were patrolling the Duomo cathedral and other sensitive sites such as the United States consulate and the city's synagogue.
While on the island of Lampedusa, where thousands of migrants have arrived from Africa in recent months seeking to enter Europe, 70 air force troops will replace the police who normally patrol the perimeter of the reception centre.
But Mario Marazziti, a spokesperson for the Sant'Egidio community which works with immigrant groups in Rome, told Al Jazeera that there was little need for the measures as Milan or Rome were much safer than other cities in Europe.
|Marazziti rejects the government's claims that Italy's streets are not safe
"We have fewer robberies in apartments in Italy than the UK and we have fewer homicides than the rest of Europe. Italy is absolutely a safe country, a great country. So we are launching a terrible message abroad and people are confused,"he said.
Marazziti said there was a complete difference between "reality and the perception of citizens".
"This is the result of years of preaching from the Northern League [a right-wing populist party] or from electoral campaigning which has been focusing on security," he said.
"So every Italian is convinced he's safe and that where he lives is safe – but that Italy is not safe … it's a real paradox and the perception is that we need more security."