A 63-year-old woman, who had suffered chronic illness, died of the Middle East Respiratory Syndrome on Saturday in the western city of Jeddah, and a 78-year-old man died from the disease in Riyadh, it said.
The ministry said the total number of cases diagnosed since the virus first emerged in September 2012 has reached 323, representing the bulk of infections registered globally.
Public concern over the spread of MERS mounted last week after the resignation of at least four doctors at Jeddah's King Fahd Hospital who refused to treat patients for fear of infection.
The World Health Organisation announced Wednesday that it had offered to send international experts to Saudi Arabia to investigate "any evolving risk" associated with the transmission pattern of the virus.
MERS is considered a deadlier but less-transmissible cousin of the SARS virus which erupted in Asia in 2003 and infected 8,273 people, nine percent of whom died.