The ministry said that five laboratory tests showed negative results for the disease, including most recently on Wednesday.
"Experts on infectious diseases and diagnosis have determined that he is no longer a MERS patient," the ministry said in a statement, adding that three relatives who traveled with the man showed no sign of having contracted the virus.
The man had traveled to Bangkok last month for treatment of a heart condition and was then diagnosed with the virus. He was quarantined and treated at the ministry's infectious diseases facility.
"His lungs X-ray shows much better result. The patient is also able to walk," the statement said.
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Middle East respiratory syndrome has killed 33 people in South Korea and sickened more than 180, the biggest outbreak outside the region where it was first seen in 2012.
Officials in South Korea say the outbreak has already peaked and could be defused by the end of the month. But the continued discovery of new cases has raised questions about the government's ability to control the situation.