The latest deaths of two men -- aged 58 and 61 -- put the total number of fatalities from Middle East Respiratory Syndrome at 16 since the outbreak began less a month ago.
One victim had diabetes while the other had no underlying illness, the health ministry said in a statement.
The total number of cases -- including the 16 deaths -- rose to 150, it said, adding 17 patients were in unstable condition.
Among them was a doctor who had performed CPR on an infected patient in Daejeon and one infected in Samsung Medical Centre in Seoul -- the epicentre of the outbreak where more than 70 patients, visitors and medical staff contracted the virus.
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The outbreak -- the largest outside Saudi Arabia -- started on May 20 when a 68-year-old man was diagnosed after returning from a trip to Saudi Arabia.
Since then the virus has spread at an unusually rapid pace, sparking alarm in Asia's fourth-largest economy.
The Samsung hospital -- one of the country's largest -- suspended most services Sunday to help curb the spread of the potentially deadly virus.
In Saudi Arabia, more than 950 people were infected and 412 died from the disease.
There is no vaccine for MERS which has a mortality rate of 35 per cent, according to the World Health Organization.