Dr Jones said he wanted to keep the swim warning lifted but it was clear the situation was more complex than previously thought.
"We need to take a precautionary approach because the risk to people's health, with the level of bacteria, is too high," he said.
"We apologise to everyone who uses the pond and has events planned this weekend, but we must make people aware of the risk to their health.
"The close monitoring and fluctuating levels means we have identified an issue with the pond that requires much more thorough investigation.
"We won't agree to lift the swim warning until we are confident bacteria levels have consistently returned to normal," he said.
Napier City Council (NCC) manager of communications and marketing Fiona Fraser said signs were put up this afternoon informing the public the pond was once again closed.
A number of strong leads into the cause of the contamination were being followed during the investigation conducted by Hawke's Bay Regional Council (HBRC), she said.
Anyone who saw any potentially unsuitable behaviour in regards to pollution in the area should call HBRC's pollution hotline on 0800 108 838 as soon as possible.
"People should be aware that if they see something not quite right they should call."
HBRC group manager resource management Iain Maxwell said he supported Dr Jones' decision and was ensuring HBRC science staff continued to investigate the problem to try to determine the cause.
If anyone is feeling sick after swimming in the pond they should see their doctor - and mention they had been swimming in the pond, he said.
Canoe Polo Hawke's Bay was due to host its annual Art Deco Competition at Pandora Pond this weekend but have had to move to Backpaddock Lakes in central Hawke's Bay.
Chairperson Kelly Hepburn said they received the results from the HBDHB this afternoon and put alternative plans into place immediately.
There will be about 385 players from 55 teams and a total of 1000 people including spectators at the tournament.
Anyone wanting to view the event is welcome to make their way to Backpaddock Lakes, she said.
NCC manager of sport and recreation Glenn Lucas said the swim warning meant the popular Pandora Splash Zone was also closed until further notice.
"It's very unfortunate but public safety is our number one concern."
Further test results would be available by lunchtime tomorrow and if clear the pond would be opened, he said.
The pond was previously closed on Wednesday due to a reading of 475 Enterococci per 100ml, which meant there were excessive amounts of faecal matter, either animal or human, in the water.
The two most commonly measured faecal indicator bacteria are E coli (in freshwater) and Enterococci (in marine waters).
The earlier warning was lifted on Thursday after two water sample tests came back clear.
For more information on where to go for medical care go to: ourhealthhb.nz/choose-well/where-should-i-go/, or call Healthline: 0800 611 116 for free, for advice from a trained registered nurse.
