Mr Hwang said that as there had been no new infections for 23 days, the public could be "can now be free from worry".
He also apologised for the government's much-criticised response to the virus, which has killed 36 people in South Korea, Yonhap news agency reports.
But the WHO said it was not yet declaring Mers officially over.
A spokeswoman in Manila said the WHO required 28 days without a new infection to make the announcement - twice the incubation period of the virus. The last case was confirmed in South Korea on 4 July.
South Korean Health Ministry official Kwon Duk-cheol said precautions, including screening at airports, would remain in place "until the situation comes to a formal end", AFP news agency reports.
"We still have many arrivals from the Middle East so there is always a possibility that new patients can come in," he added.
-BBC