The report also found not enough E. coli samples were taken from the Brunswick-Westmere supply.
Fordell, Maxwell and Mowhanau Beach supplies were all compliant with the Health Act and met required standards.
Whanganui District Council senior engineering officer Dave Rudolph said Whanganui's water supply used secure groundwater, which was chlorinated, and parts of the supply were treated with ozone treatment.
Rudolph said a delivery issue was the cause of the missed sample.
"The correct number of water samples was taken but in one instance the sample did not reach the testing laboratory on time because it was delayed in transit.
"Missing one test did not result in any change to the secure bore status and the safety of our drinking water."
Issues were also identified in the Rangitikei district's water drinking water.
Supply for Bulls, Hunterville, Ratana and Taihape all met bacterial and chemical standards, but failed the protozoal standards.
The report found that after an issue was discovered in Marton's supply, appropriate action to protect public health was not taken.
"Marton had one disinfection by-product that exceeded maximum acceptable values and was not appropriately acted upon," the report states.
"It therefore failed to meet the chemical standards for the whole supply."
About 4700 people get their drinking water from the supply.
Not enough E. coli samples were taken from the Mangaweka supply resulting in a failure to comply with the Health Act.
The supply also failed overall standards by not meeting protozoal requirements.
Rangitikei Mayor Andy Watson said the supply of water was something council took seriously.
"We have spent a lot of money in the last Long Term Plan and projected to continue spending on new water plants along with the connecting infrastructure such as pipes to service it," he said.
"Like much of the country a lot of the water systems were designed 60 to 100 years ago and they've run their length of time so it's a need to replace pipes."
Watson said the council was looking at ways to deliver a better service, especially for Bulls and Marton.
"Most of the failed standards like the rest of the country are where there may have been inefficient reporting or a technical breach, rather than any other breach.
"It is disappointing and we can say we'll sort some things but at the end of the day we need to comply with the systems that are there and we'll need to continue to improve."
Nationally, 97 per cent of the population received water that achieved bacteriological standards and 92 per cent received water that met all monitoring requirements.
"Overall, conclusions from the report are that most New Zealanders receive safe drinking water, " Ministry of Health's director of public health Dr Caroline McElnay said.
"However, some people, usually those in rural areas or smaller supplies, can't always access water of the same standard."
McElnay said the ministry had written directly to suppliers who were failing to comply with the act.
