The warning means South Korea is considered to pose significant threats to tourism, and Hong Kong residents are advised to cancel non-essential travel.
South Korea confirmed a seventh death from the Mers infection on Tuesday, and 95 infections.
The outbreak is the biggest since Mers was first detected in the Middle East.
The latest victim was a 68-year-old woman with a pre-existing heart condition. She was infected at the same hospital as all the other victims so far.
Middle East Respiratory Syndrome (Mers)
How dangerous is Mers?
In pictures: How Seoul is dealing with outbreak
The Hong Kong red alert is its second-highest level, and says people should "avoid non-essential travel to Korea, including leisure travel".
The warning said anyone who did still visit South Korea should "avoid unnecessary visit to healthcare facilities" and take precautionary measures, including wearing a mask and washing hands.
Ko Wing-man, secretary for Food and Health Bureau, said the measures had been taken in part because of the "frequent communication between Hong Kong citizens and South Koreans".
Hong Kong was badly hit by the Severe Acute Respiratory Syndrome (Sars) outbreak in 2003, which was brought to the territory from Southern China by a doctor, so it is sensitive to new disease threats.
Eight new Mers cases were confirmed in South Korea on Tuesday, a significant drop from the 23 new cases reported on Monday.
The South Korean government believes the fact that all cases have been linked to hospitals which treated known patients means the virus can still be contained.  All the fatalities have been people who were already unwell.
As of Monday, 2,500 people who may have come into contact with the virus were under quarantine, said the Yonhap news agency, and nearly 1,900 schools have been closed.
The first Mers case in South Korea was a man who became infected during a business trip to Saudi Arabia, where the disease was first identified three years ago.
Medical authorities have been criticised for the way they have handled the outbreak.
Seoul Mayor Park Won-soon accused central government of not providing enough information to citizens about the virus. But Health Minister Moon Hyung-pyo rejected the claim, saying such comments risked increasing public concern.
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Police, fire crews, flood wardens and water and electricity engineers are taking part in the scenario.
Natural Resources Wales (NRW) said the role play will test evacuation drills.
Margaret Hughes, 91, died when the small north Wales city was inundated after the River Elwy overflowed in November 2012.
The case prompted a major overhaul of emergency evacuation procedures.
Mrs Hughes' inquest this month heard the vulnerable pensioner drowned in her Denbighshire home after she refused to leave despite flood warnings.
The hearing was told how Mrs Hughes was registered to received flood alert warnings, but her family did not receive them.
It also heard how rescue teams had to swim to homes submerged by the River Elwy deluge.
NRW said the multi-agency exercise on Wednesday and Thursday would see how the emergency services and local authority would respond to a similar flooding incident.
It said the operation would involve both a table-top exercise and live role play - including issuing flood alerts and warnings, putting up removable flood defences and testing the flood warden network.
North Wales director of operations for NRW Tim Jones said: "The flooding in 2012 was devastating for people in St Asaph, destroying homes and businesses, damaging infrastructure and unfortunately ending with tragic consequences for one family.
"We've been working hard to support the community in the aftermath of the flooding, and to make sure the city is better prepared to cope with flooding in the future.
"We've already made huge headway in improving flood protection, but this exercise will be a vital test of the plans we've made, and how all the agencies involved come together to work quickly and efficiently to protect people in such an emergency."
Hong Kong has issued a red alert warning against travel to South Korea, which is battling an outbreak of Middle East Respiratory Syndrome (Mers).
[NEXT_CONCEPT]
Flood defence plans for St Asaph are being tested in an exercise, two years after it was swamped when a river burst its banks, killing an elderly resident.