Thirteen new cases were also confirmed, expanding the list of known cases to 108 following the diagnosis of the first infected patient on May 20, the health ministry said.
The two latest fatalities include a 75-year-old woman and a 62-year-old man, both victims of the largest outbreak of the virus outside Saudi Arabia.
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The three other new victims had their diagnoses confirmed at three different hospitals, including two in the central city of Daejeon and one near a southern suburb of Seoul.
All the infections were limited to hospitals and health authorities stressed that the outbreak had not spread to communities outside hospital settings.
The nine dead people had pre-existing health conditions, the ministry said.
The virus is considered a deadlier but less infectious cousin of Severe Acute Respiratory Syndrome (SARS), which killed hundreds of people when it appeared in Asia in 2003.
There is no vaccine or cure for MERS which, according to World Health Organisation (WHO) data, has a fatality rate of around 35 per cent.
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