UPDATE, 1.30pm: Coliban Water has assured customers drinking water in flood-affected townships is not the issue as gastro spreads through communities.
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A spokesperson said the drinking water in places such as Echuca and Rochester is currently safe to consume.
"We continue to focus on operations at Echuca, including flushing the network, to resolve the increased levels of manganese in the supply network," they said.
"Customers should notice improvements to the clarity of their water in the coming days.
"A reminder, warm damp conditions create an environment where bacteria and germs can spread quickly.
"If you come into contact with floodwater or are cleaning-up flood-impacted areas, please practice good hygiene.
"Wash your hands thoroughly with soap and water regularly, particularly prior to eating."
Earlier: State authorities have issued a warning urging residents to keep away from floodwater as some exposure could make them "very sick".
The State Emergency Service stated "many" cases of gastroenteritis and diarrhoea had emerged and locals should avoid contact to prevent illness. People should also wash their hands after going to the toilet, before eating, preparing food and cleaning.
"Floodwaters may contain sewage and other toxic waste and can also overflow into your home," the authority wrote.
"Contact with sewage can make people sick, so clean and disinfect any impacted areas."
Residents warned about a number of diseases
With more still water laying around, authorities are also warning residents to cover up in order to protect themselves against the growing mosquito population.
Bendigo Health chief executive Peter Faulkner said the Loddon Mallee Public Health Unit was working to assist these communities.
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"It's been incredibly wet, and with that comes heightened risk of mosquito breeding and mosquito-born diseases," he said.
"Japanese encephalitis virus (JEV) is one, but there are many others we should be concerned about.
"We would encourage everyone in the community to cover up, utilise mosquito protections and be really vigilant and careful."
Vaccines available to combat JEV
Mr Faulkner said there was a limited supply of vaccines for JEV and there were criteria for its administration.
"You must be over 50 years of age, in a risk zone and spend at least four hours a day outside either working or in recreation," he said.
"Our role is just one of providers of vaccine services, so we're working to particularly target vulnerable populations, those who are less-able to access care.
"We're working with providers such as Indigenous-controlled health organisations to support them, community health and a range of others."
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