The president of the Samsung Medical Center in the capital Seoul issued a public apology on Sunday.
Health officials have reported seven new cases bringing the total to 145. Fifteen people are known to have died.
Meanwhile, a South Korean man in Slovakia is being tested for the virus.
The man reportedly works for a subcontractor of South Korean car maker Kia.
Samsung Medical Center president Song Jae-hoon told reporters that the hospital would stop treating outpatients and admitting new patients to prevent further infections among patients and medical staff.
He said no visitors would be allowed, and non-urgent surgery was being stopped.
"We apologise for causing great concern as Samsung Medical Center became the centre of the spread of Mers," he said.
"This is entirely our responsibility and failing, as we did not properly manage emergency-room staff."
Mr Song said he would review the suspension on services on 24 June.
More than 70 cases have been traced back to the hospital, authorities say.
Among them was an emergency ward orderly who worked for days after developing symptoms and came into contact with more than 200 people, officials said.
It is believed the orderly picked up the virus from an infected person who waited for days in various parts of the emergency ward, potentially exposing the virus to an estimated 900 staff, patients and visitors.
South Korea reported seven new cases on Sunday and the 15th victim died in the city of Busan.
The World Health Organization (WHO) has warned that the outbreak is "large and complex" with further cases expected, although it does not expect the outbreak to spread among the wider community.
The outbreak is the largest outside Saudi Arabia, where the disease was first identified in humans in 2012.