A woman aged 69 died in Riyadh and a 55-year-old man died in the city of Mecca, home to Islam's holiest site which is visited by millions of pilgrims each year.
A fifth man, 59 died on Sunday in the western city of Taif.
The ministry said the total numbers of infections has reached 537 case.
Other nations including Egypt, Jordan, Lebanon, the Netherlands, the United Arab Emirates and the United States have also recorded cases, mostly in people who had been to the desert kingdom.
MERS is considered a deadlier but less transmissible cousin of the SARS virus that appeared in Asia in 2003 and infected 8,273 people, nine percent of whom died.
Like SARS, it appears to cause a lung infection, with patients suffering coughing, breathing difficulties and a temperature. But MERS differs in that it also causes rapid kidney failure.