The ministry announced the new figures on Saturday, but said one patient had recovered, becoming the first to be discharged from hospital.
The outbreak, which was first reported on May 20, has claimed four lives and stirred much public fear as the government was blamed for an ineffective initial response that allowed one man who had returned from Saudi Arabia to infect more than half of the rest.
All nine new cases were traced to the initial patient, the health ministry said, calling them healthcare associated infections.
The nine included one healthcare worker at a hospital that treated an infected patient, it said.
There has been no sustained human-to-human transmission, but the worst case scenario is that the virus changes and spreads rapidly, as Severe Acute Respiratory Syndrome (SARS) did in 2002-2003, killing about 800 people around the world.
Al Jazeera's Harry Fawcett, reporting from Seoul, said more than 1,000 schools suspended classes during the week and education officials say they will close all schools in the capital's southern Gangnam district from Monday unless the situation improves.
Fawcett said that while South Korea is far from being in a state of panic, the number of face masks being sold in pharmacies has increased seven-fold over the past week.
Choi Jae-Wook, an official at the Korean Medical Association, said: "This weekend will be critical. The incubation period for primary and secondary patients ends this weekend.
"If there is no further infection, then we can say we have stemmed the main tide.
"But if there are more cases, we will have to prepare for tertiary and fourth generation infections - and the spread into the local community."
MERS was first identified in humans in 2012 and is caused by a coronavirus from the same family as the one that triggered SARS.
However, MERS has a much higher death rate at 38 percent, according to World Health Organisation (WHO) figures.
South Korea's new cases bring the total number globally to about 1,194, based on WHO data, with at least 443 related deaths.