Around 50 of the zoo's 69 Humboldt penguins have so far died after the avian disease tore through the colony despite a major effort from vets and the zoo's bird keepers.
The parasitic disease is transmitted by the bite of infected mosquitoes. It can't be passed on to humans or other animal species but can be fatal to penguins who do not have a natural immunity to the disease.
Derek Grove, the zoo's director, said: “We are all heartbroken with the huge loss in Penguin Bay and it’s been an especially distressing time for our bird team who have devoted years to their care.
“Their dedication and tireless efforts to care for our penguins over recent weeks has been exemplary.
"They’ve provided round-the-clock care to individually treat the birds in their fight to save as many as possible and we thank them for their determination.
“Having consulted with avian experts and animal collections around the world, we know we’ve done all we can.”
The zoo, including the Penguin Bay area remain open, but around 70 per cent of the penguin population has died, a spokesman confirmed.
Zoo keepers are immensely sad at the loss, having successfully bred the Humboldt penguins over the last 30 years.
The zoo started out with just five hand-reared chicks in 1991 and went on to have one of the largest self-sustained colonies in the country, with many of the penguins helping boost new groups at collections around the country.
Mr Grove added: “Thankfully occurrences like this are rare and in over three decades we’ve never experienced anything like it before.
“Unfortunately, penguins are particularly susceptible to the disease as they do not have natural resistance against it and it’s also not easily identifiable through medical tests.
“We do not know if last year’s unusual weather pattern has played a part, with wet and muggy weather not only impacting the penguin’s moulting season, but also increasing the risk of mosquitos, but what we do know is we now need to focus on continuing to treat the remaining birds and putting in place additional preventative measures to avoid this tragedy happening again.”