The Ministry of Health's recently released Drinking Water Quality report for 2017-18 shows of 55 water supplies in the region 48, or 87.3%, did not reach Drinking-water Standards for New Zealand, compared to 33% nationally.
Twenty-two, or 40%, did not reach drinking water standards under the Health Act, compared with 33.3% nationally.
The previous year's report is compiled differently so is difficult to compare by region.
Drinking-water Standards for New Zealand relate mostly to bacteria and protozoa levels and monitoring.
Health Act requirements cover the provision of drinking water, source protection, record keeping, complaints responses and remedial action.
In Otago, the Waitaki District Council has the lowest pass rates with two of 12 supplies meeting Health Act standards and none meeting drinking water standards.
Oamaru, which serves 14,390 people, is the largest supply in the region to not meet either standard.
Waitaki District Council water services and waste manager Martin Pacey said most of the reasons for its low pass rates were "technical in nature''.
Issues arose with its courier being unable to supply samples in the required 24-hour timeframe, but this had now been remedied.
All water supplies which had a water treatment upgrade were safe to drink, however, there were still some yet to be upgraded, he said.
The Central Otago District Council's nine supplies all met Health Act standards, but failed national drinking water standards because of protozoa levels.
Council infrastructure services executive manager Julie Muir said it committed $23million to a programme of work to provide protozoa treatment to all Central Otago District Council water supplies by 2023.
The Dunedin City Council has four supplies which all meet Health Act standards and all except the main Dunedin supply, serving 112,515 people, reached drinking water standards.
The Dunedin supply failed because it exceeded acceptable E.coli levels.
Council 3 waters planning manager Zoe Moffat said the problem was with one of the council's taps, which led to two consecutive positive results for E.coli, despite the drinking water being fine.
"Following the results, the DCC is installing purpose-built sample taps across the city which will improve the reliability of water quality test results.''
For the Clutha District Council and Queenstown-Lakes District Council, seven out of 14 supplies and nine out of nine supplies respectively met Health Act standards.
No supplies from either council reached drinking water standards.
Neither council was able to directly answer questions yesterday.
University of Otago public health professor Michael Baker said while contaminated drinking water could be a concern, it depended on why supplies were failing.
"It could just be a bird crapping, or something more significant.
"Either way it's certainly a warning some sort of action needs to be taken.''
In some cases, like that of campylobacter, it would be more effective from a public health perspective to tackle other causes such as infection in chicken rather than spending money on water upgrades.
"Let's deal with the things that are really making people sick in this country and work down the list.''
