An official statement said health workers had detected an increase in “watery diarrhoea” in some districts, which has been established as cholera.
The source has been identified as a foodseller who caught cholera during a previous outbreak in eastern Cuba.
Doctors have been going house to house in Havana areas, checking for symptoms.
The official confirmation follows several days of speculation about an upsurge in diarrhoea in the capital, where a 46-year-old man died of suspected cholera earlier this month.
In the central Havana district of Cerro, where the outbreak is believed to have begun, cafes and restaurants have been closed and only the sale of sealed food and drink is permitted.
The outbreak was detected on January 6. According to the health ministry, measures taken since then mean the disease is in its “extinction phase”.
People are being urged to take care with hygiene and in the preparation of food.
Cholera is carried by contaminated water or food. It causes severe dehydration through diarrhoea and can prove fatal if untreated.
Until last July, Cuba had not experienced any significant outbreak since well before the 1959 revolution.
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