The health ministry's daily bulletin on the Middle East Respiratory Syndrome outbreak in the Gulf nation said the latest people to die were two women aged 72 and 54 and a 63-year-old man.
Since MERS first appeared in Saudi Arabia in 2012 the authorities have recorded 514 infections from the mystery virus for which there is currently no known antidote.
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.
The WHO called on countries to improve infection prevention and control, collect more data on the virus and to be vigilant in preventing it from spreading to vulnerable countries, notably in Africa.
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But it has so far stopped short of declaring an international health emergency, which would have far-reaching implications such as travel and trade restrictions on affected countries.
A WHO team carried out a five-day inspection visit to Saudi Arabia earlier this month and pinpointed breaches in its recommended infection prevention measures as being partly responsible for the spike in hospital infections.
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 Severe acute respiratory syndrome (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.