The ministry said the doctor, the first Italian to contract the disease, would arrive in Rome late Monday or early Tuesday and be hospitalised at the Lazzaro Spallanzani national institute for infectious diseases.
The doctor was working for NGO Emergency at a clinic for Ebola victims when he contracted the disease, which has killed more than 5,000 people in its latest outbreak in West Africa.
"We can reassure his family that the doctor is feeling well," health minister Beatrice Lorenzin said in a statement.
"He did not have a fever or other symptoms during the night and this morning he had his breakfast."
The NGO said the doctor had developed some unspecified Ebola symptoms but was in a "good general condition."
The more serious symptoms of Ebola can take weeks to develop.
Emergency said all its staff in Sierra Leone had been trained to avoid contamination.
"However no healthcare in such a serious epidemic can be considered completely risk-free," the NGO said in a statement.
"The situation in Sierra Leone is alarming: the epidemic is still widening with 100 new cases a day. According to the World Health Organisation there are more than 5,000 people with Ebola in the country but the real figures could be much higher."
The doctor is the first Italian to be infected with the disease, although there have been a number of health scares in recent months.
The virus has also sparked panic, with a three-year-old being banned from a school in Rome last month over fears she caught the disease during a holiday in Uganda.
There was also uproar in late October after it was revealed that US troops returning from West Africa were being quarantined at a base in Vicenza as a precaution to prevent the potential spread of the virus.
The Italian government said in October it would contribute €50 million to an EU fund set up to fight Ebola.
Figures released by the WHO on Friday put the number of cases registered in Sierra Leone at 6,190, with 1,267 deaths.
The former British colony has been among the countries worst affected by the outbreak of one of the deadliest viruses known to man, along with Liberia and Guinea.
Emergency is a humanitarian organisation founded by celebrated heart surgeon Gino Strada which specialises in providing medical care including emergency operations in conflict and crisis zones.
As well as its clinic in Freetown, Sierra Leone is has operations in Afghanistan, the Central African Republic, Iraq and Sudan, among others.
Meanwhile, a Swedish health expert said on Monday that the threat of the virus has decreased and suggested that the battle against the epidemic is entering a new phase.
Hans Rosling, Professor of Global Health at Karolinsta Institutet, said the number of new cases in recent months indicated that the virus was not spreading as much as previously anticipated, according to a report on The Local Sweden.