"Today at 20:44 (19:44 GMT) we were notified of the first case of coronavirus. The patient returned from Morocco through Italy, he has currently been hospitalized to an infectious diseases clinic in Ljubljana", the ministry said on Twitter on Wednesday.
All possible contacts of the patient in Slovenia are being checked, it said.
Worldwide, over 95,000 cases have been reported, with 51,100 people having recovered and 3,254 having died from the illness since it was identified in Wuhan, China, in December 2019.
According to the World Health Organization, the disease has a mortality rate of about 3.4%, roughly equivalent to that of pertussis, also called whooping cough.