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 travelled with the man showed no sign of having contracted the virus.
The man had travelled 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.
He remains in a weakened state, but the ministry said his condition was improving. It said he had been able to breath without a ventilator for five days.
"His lungs X-ray shows much better result. The patient is also able to walk," the statement said.
Middle East respiratory syndrome has killed 24 people and sickened more than 160 people in South Korea, 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.
MERS belongs to the family of coronaviruses that includes the common cold and SARS, and can cause fever, breathing problems, pneumonia and kidney failure. Most of the deaths in South Korea have been of people suffering from pre-existing medical conditions, such as respiratory problems or cancer.