"This is an indication that there's been some faecal matter ... we're trying to figure out if it washed in from heavy rain."
However, because it hadn't quickly dissipated, there might have been another cause for the high levels such as a nearby septic tank, he said.
Signs had been put up by HDC and HBDHB would be testing again today.
"Regular water sampling and monitoring will continue and Hawke's Bay Regional Council will also investigate the source of the contamination."
People should take notice of the warnings and avoid swimming in the lagoon until further notice, Dr Jones said.
In parts of the Tukituki River Cyanobacteria mats had been exposed because of a drop in river level and warning signs were put in place on Friday.
"People are urged to keep dogs and children away."
The algae was likely to be toxic to people and animals.
Cyanobacteria blooms were more common in warm weather and during low flows and tended to be worse in summer, Dr Jones said.
"The Tukituki River has had this bacteria in it before.
"A couple of spots have been identified where the levels are dropping and the Cyanobacteria mats have been exposed, such as Black Bridge, Red Bridge and Horseshoe Bend.
"The rest of the river levels of Cyanobacteria are fine."
The bacteria would most likely wash away after a heavy rainfall but if anyone saw it in the river they were advised to keep away from that area.
"The issue is that it can produce toxins."
These can kill dogs and make people feel sick with flu-like symptoms.
It can also produce an odour which attracts dogs.
The exposed areas were more risky than if the bacteria was under the surface of the water where it was less likely to come in contact with people or dogs, Dr Jones said.
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