The two most commonly measured faecal indicator bacteria are E. coli (in freshwater) and Enterococci (in marine waters).
Dr Jones said people needed to heed health official advice and avoid any contact with the water.
"People should not swim, or undertake any other water based recreational activities in Pandora Pond until further notice.
Dr Jones said swimming and water based activities in contaminated water poses a risk of infections of the stomach, skin, eyes and ears.
When the notification was received Council advised its team at Splash Zone and notified the environmental health team that signs needed to be put out, council communications and marketing manager Fiona Fraser said.
"We are awaiting the next test results. It's possible that the level will have dropped with incoming and outgoing tides," she said.
Napier City Council Manager Sport and Recreation, Glenn Lucas, said organisers planning upcoming events at Pandora Pond were being notified. The Pandora Splash Zone's inflatable water playground would also be closed until further notice.
Napier City Council's Director of Infrastructure, John Kingsford, said there had been no known discharges of wastewater into the pond that could have caused the high reading.
Hawke's Bay Regional Council Water Quality Technician Shane Gilmer said the high reading was picked up in a regular weekly sample. Staff have since done two consecutive re-samples, which have been sent away for testing. Results were expected in the next 48 hours.
He said when sampling the pond this week he noticed the water was very discoloured. "Generally as a handy guide - if people can't see their toes when standing in knee-deep water, then water-quality is not the best for a swim".
Mr Gilmer said there had been rain within the catchment in the last week which had contributed to surface water runoff, which then entered the estuary.
City Council chief executive Wayne Jack said they are looking forward to the development of the Ahuriri Estuary Management Strategy in conjunction with Mana Ahuriri to ensure the long term sustainability and health of the Estuary that will address a range of issues including water quality.
Napier Mayor Bill Dalton said he was only advised of the matter late in the afternoon and had no further comment to make.
