"We strongly advise you to avoid excursions outside of tourist areas, particularly in cities," the foreign ministry said in a statement on its website on Thursday.
The ministry also said the security situation in the northern part of the Sinai peninsula was "very precarious" and advised against any travel there.
"There is a risk of terrorist attacks. There should be particular caution in the region bordering the Gaza Strip, in Cairo and Alexandria," it said.
"Great prudence is recommended in crowded areas".
Wednesday's violence, which came as security forces stormed the protest camps of supporters of Mohamed Morsi, has left at least 370 dead across Egypt, according to official estimates.
There are currently around 19,000 Italians in Egyptian resorts – 5,000 more than last week at the height of the holiday season in Italy, ANSA news agency reported.
Fortunato Giovannoni, head of the federation of Italian tour operators Fiavet, said on Tuesday that there had been an 80-percent drop in Italian tourists in Egypt this year from the same period in 2012.