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 disease.
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.
The NGO said the doctor had developed some unspecified Ebola symptoms but was in a "good general condition."
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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.