The man was one of more than 120 passengers and crew evacuated from the Dutch-flagged MV Hondius, whose fate has sparked international alarm after three passengers died.
A military hospital in Madrid is quarantining 14 Spaniards who were removed from the vessel on Sunday, with all but one testing negative for hantavirus.
READ ALSO: Spain says it took 'all measures' to stop hantavirus amid new positive cases
"The patient who provisionally tested positive for hantavirus yesterday has been confirmed as positive," the ministry said, without providing more details on his identity.
"Yesterday the patient had a slight fever and minor respiratory symptoms, although at present he is stable and without any evident clinical deterioration."
Among living patients, all passengers or crew from the ship, seven cases have been confirmed and an eighth is listed as "probable", according to an AFP tally of official figures.
Fortunately, two women hospitalised with a suspected hantavirus infection in Barcelona and Alicante have tested negative on their PCR tests, but they will be kept in quarantine for the time being.
The rare Andes variant of the virus, which usually spreads among rodents, is transmissible between humans and has no vaccine or treatment.
Yet health officials have stressed that the risk to public health is low and rejected comparisons to the Covid-19 pandemic.
READ ALSO: WHO chief says 'work not over' after hantavirus evacuation in Spain
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