"We... instead invite Italians to maintain the maximum caution, maintain physical distancing, avoid large groups, to frequently wash their hands and to wear masks, " an Italian Health Ministry representative said in a statement.
But the government has insisted this is one of the most risky phases of a pandemic that has claimed 33,500 lives in the country.
"We have never said that the virus has changed, we said that the interaction between the virus and the host has definitely changed", the doctor told the media.
Italy has the third highest death toll in the world from COVID-19, with 33,475 deaths and 233,197 confirmed cases as of Tuesday, according to data from Johns Hopkins University.
With the country facing its deepest recession since World War II, it needs a swift return of foreign tourists.
The doctor cited a study at San Raffaele which compared samples of COVID-19 patients admitted in March with that of those infected in May.
But it is still reporting hundreds of new cases a day, particularly in the northern Lombardy region, and experts warn the government may be moving too quickly in permitting travel between regions and overseas.
Worldwide flights were only expected to resume in three main cities: Milan, Rome and Naples.
Italy fears those who usually travel in by vehicle, train or ferry may holiday elsewhere.
Arrivals in Italy from Europe will not be required to self-isolate unless they have recently travelled from another continent.
Lockdown had a devastating effect on Italy's tourism sector which amounts to some 13 percent of GDP.
Historic sites were shut, restaurants closed, and hotels were used to care for coronavirus sick.
Restaurants, cafes and beach establishments have slowly reopened over the past two weeks - although the government has said it reserves the right to impose localised lockdowns if it sees contagion numbers rise.
Only 40 of Rome's 1,200 hotels have reopened, the Corriere della Sera newspaper said, and just a dozen in Milan. It costs too much to open them if they will just stand empty.
Infectious diseases expert Massimo Galli said it would have been better to wait until July to reopen the borders.
Italy's national tourism agency (ENIT) said some 40% of Italians traditionally travel overseas for their holidays, but could be forced this year to vacation at home, helping local businesses.
Switzerland has warned its citizens that if they go to Italy they will be subject to "health measures" on their return. The country will open its borders with Germany, France and Austria on 15 June, but not with Italy.
Other countries, such as Belgium and Britain, are still advising against, or forbidding, all non-essential travel overseas.
The coronavirus "may now be different: the firepower it had two months ago is not the same firepower it has today", he said.