The Middle East Respiratory System coronavirus has now infected 483 people in the Gulf nation since it first appeared in 2012, accounting for the vast majority of the 496 cases registered worldwide.
In its daily bulletin, the ministry said a 45-year-old man had died from MERS in Jeddah on the west coast, and two women aged 60 and 62 died in the capital, Riyadh.
The announcement came as the World Health Organisation prepared for an emergency meeting to discuss the disease on Tuesday.
The UN health agency's emergency committee has already met four times to discuss the mysterious coronavirus.
MERS is considered a deadlier but less-transmissible cousin of the SARS virus that broke out in Asia in 2003, infecting 8,273 people and killing nearly 800.
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.
Although most MERS infections have been in Saudi Arabia, cases have also been recorded in the United Arab Emirates, Jordan, Egypt, Lebanon and even the United States.
Most cases outside Saudi Arabia involve people who had traveled to the kingdom or worked there, often as medical staff.