The victim was a 73-year-old Saudi man, who suffered from chronic illnesses, the ministry said on its website.
It also reported three new cases of the virus.
They are two foreigners working in health care who had been exposed to patients suffering from the virus and a 53-year-old Saudi man who is also chronically ill and in intensive care.
The ministry said 136 cases have been reported in the country since the virus appeared more than a year ago.
Experts are struggling to understand the disease, for which there is no vaccine.
It is considered a deadlier but less-transmissible cousin of the SARS virus that erupted in Asia in 2003 and infected 8,273 people, nine percent of whom died.
Still warning people to take it easy with travelling.