Threats to Canterbury's drinking water are a "ticking time bomb" that could lead to infant deaths if not more strictly controlled, a top health official has warned.

Environment Canterbury's (ECan) 2012 groundwater survey, released this month, found nitrate levels had been increasing in about 30 per cent of tested wells - the main source of drinking water in rural areas - in the past 10 years.

Ashburton was the most at risk, with 20 wells tested exceeding safe nitrate levels.

Canterbury District Health Board medical officer of health Alistair Humphrey yesterday warned a baby could die if nitrate levels were not more tightly controlled, calling it a "ticking time bomb".

Of the 289 wells tested last year, 33, or 11 per cent, had nitrate levels that exceeded the maximum acceptable value for drinking water standards - 4 per cent higher than the previous year.

No trend was found in 67 per cent of wells, while 3 per cent showed a decreasing trend.

Banks Peninsula was not tested.

Humphrey was concerned as nitrate levels could cause methaemaglobinaemia in infants.

The condition affects blood by converting a substance to a chemical that cannot deliver oxygen to tissues. It occurs after consumption of nitrates either during pregnancy or by bottle-feeding.

While no confirmed cases have been identified, there had been reports of mothers claiming their babies had been affected by groundwater.

The health board has been working with maternity carers in the Ashburton area to ensure pregnant women and parents know the risks of consuming water with high nitrate levels.

"It's a ticking time bomb.

"Sooner or later, a mother will not be aware of her water supply and she might make up some formula and that might lead to a tragedy," Humphrey said.

The Ashburton water management zone committee needed to deal with the increasing nitrate levels as it would likely to take decades to reverse the upward trend, he said.

"We know that clean farming is possible but clearly it is not happening."

ECan groundwater quality team leader Carl Hanson said the increased nitrate levels reflected the intensification of farming across the region.

"What leaches out is a pretty small percentage but that's all that it takes," he said.

However, not all elevated levels were because of farming with some increased concentration linked to specific discharges such as meatworks wastewater northeast of Ashburton.

Ashburton water management zone committee chairman Matthew Hall said dealing with nitrates was "at the top of the agenda".

The committee was working on recommendations for the Canterbury Land and Water Regional Plan, which was before hearing commissioners.

"At the moment it is work in progress ... it will mean farmers will need to achieve good farming practices."

Hall said it was not a quick fix but hoped to have all farmers complying with specific nitrate limits by about 2017.

Federated Farmers Mid-Canterbury president Chris Allen said the organisation was working with the zone committee on quantifying and identifying the problem, and finding solutions.

"There's a lot of work starting to happen ... farmers are definitely taking it seriously," he said.

Ashburton Mayor Angus McKay was waiting to see what the committee's plan was but said he was "well aware" of the seriousness of the situation.

CANTERBURY WATER NITRATE LEVELS

Number of samples not meeting drinking water standards, in terms of nitrate, for the 2012 annual survey.

Total number of wells tested: 289

Total number exceeding safe nitrate level: 33

Ashburton: 20.

Christchurch-West Melton: 0.

Hurunui-Waiau: 2.

Kaikoura: 0.

Lower Waitaki/South Coastal Canterbury: 2.

Orari Opihi Pareora: 5.

Selwyn-Waihora: 3.

Upper Waitaki: 1.

Waimakariri: 0.