A Saudi man, aged 74, died in the western city of Medina after being in contact with an infected person, the ministry said on its website.
A 56-year-old foreigner, who worked in the health sector, also died in Medina, while another Saudi, aged 53, who suffered chronic diseases, died in Riyadh, the ministry added.
The health authority also announced five new cases of infection of the coronavirus, including an 18-year-old Saudi man, and a three-year-old girl in Hafr al-Baten, in the northeast, who contracted the virus after being in contact with an infected person.
The three others are all Saudi nationals.
Saudi Arabia is the country worst hit by MERS, which has killed 47 in the kingdom. On Friday the World Health Organisation said the virus had killed 52 people worldwide. Saudi authorities said 96 people have been infected in the kingdom, out of a global figure of 110.
Experts are struggling to understand MERS -- Middle East Respiratory Syndrome -- for which there is still no vaccine and which has an extremely high fatality rate of more than 51 percent.
It is considered a cousin of the SARS virus that erupted in Asia in 2003 and infected 8,273 people, nine percent of whom died.
Like SARS, MERS is thought to have jumped from animals to humans, and it shares the former's flu-like symptoms -- but differs by also causing kidney failure.
The MERS problem persists in Saudi Arabia as the kingdom gears up to host around two million Muslims in October for the annual hajj pilgrimage to Mecca.
Authorities have urged the elderly and chronically ill Muslims to avoid the hajj this year and have cut back on the numbers of people they will allow to perform the pilgrimage.
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