Recent samples from one of Meridian's Manapouri power station cooling water units tested positive for the lake snow algae, prompting Environment Southland to urge water users to keep their equipment clean.
Environment Southland senior biosecurity officer Randall Milne said monitoring had also been carried out in Te Anau but lake snow had not been detected there.
"It's important that we protect our waterways from all freshwater pests by being very careful when moving from one waterway to another.
"People need to follow the check, clean, dry actions for all boats and equipment being transferred from one area to another, to ensure they are not carrying anything unwanted."
The algae, which is present in lakes including Wanaka, Wakatipu and Hawea, had not been found in New Zealand before 2001.
"At this stage there is no silver bullet for getting rid of lake snow."
Although not toxic, it can become a costly problem if it gets into residential water supply where it causes blockages, clogs filters and household appliances.
