This threshold was also crossed at 91 per cent of pastoral sites, 46 per cent of exotic forest sites and 29 per cent of "natural" areas of native forest.
About half of New Zealand's river length is fed by catchments that are mainly influenced by indigenous land cover, while 45.7 percent are influenced mainly by pasture, 5.1 percent by exotic forest, and 0.8 percent by urban land cover.
Overall, the mean level of colony-forming units (CFU) of E .coli per 100mL of water was 44.1 CFU in natural areas, 114.2 CFU in areas of exotic forest, 258.4 CFU in pastoral areas and 671.5 CFU in urban areas.
A commonly-used standard for safe recreational use of water, since generally replaced in New Zealand by a two-step indicator, was 126 CFU per 100mL.
In lowland sites, mean levels were much higher: 156.5 CFU in natural areas, 209.1 CFU in exotic forests and 334.5 CFU in pastoral sites.
But an E. Coli risk of "secondary contact" with rivers - such as wading or boating - only affected two per cent of all sites.
Scientists trying to tease out clear patterns of E. coli contamination in rivers have long been hampered by a lack of data and the complexities of trying to interpret trends.
But study co-author and NIWA water quality scientist Graham McBride said of those sites that could be compared, more appeared to be improving than deteriorating.
Of 396 regional council sites monitored between 2004 and 2013, 54 had increasing concentrations and 81 had decreasing concentration.
A trend could not be determined for 261 sites.
"So there's a fairly large category where we haven't got enough data to tell, because of variability," McBride said.
"However we are looking at some new statistical approaches that will mine more trend information from this rather large proportion of sites.
Read More: Why are our rivers and lakes becoming unsafe?
"As microbes tend to change their concentrations more rapidly than nutrients and sediment, for example, is it a bit harder to detect what's happening."
McBride believed keeping cattle out of streams by fencing off waterways would have brought benefits in rural parts of the country.
The dairy sector has reportedly spent more than $1 billion on measures to protect waterways, and from May will be subject to requirements under its Water Accord, prohibiting all stock from any permanently flowing rivers, streams, drains and springs, more than a metre wide and 30cm deep.
According to Dairy NZ, more than 96 per cent of waterways on New Zealand dairy farms were now excluded from dairy cattle.
"On the other hand, however, we've now got more of some animals than we used to have, which means there is more being deposited on the land," McBride said.
"It's a complicated story and there may well be a new study initiated nationwide to get a better handle on all of it, including pathogens."
While E. coli levels could spike during high rainfall events - when faecal material was washed off land, triggered no-swim warnings, high concentrations could also be caused by animals defecating directly into low-flowing rivers.
"The main point is that we must never be complacent about microbial contamination - and I think what happened in Havelock North has given us plenty of grounds for re-enforcing that view," he said.
"We always need to be vigilant."
People could check the latest state of their local river at through the Land Air Water Aotearoa website.
E. Coli
*E. coli is a group of bacteria commonly found in the intestines of warm-blooded animals, including people, and, when found in excess in fresh water, can indicate the presence of disease-causing organisms, or pathogens, from animal or human faeces.
*Most strains of E. coli are harmless, but some could make people sick, cause severe stomach cramps, diarrhoea and vomiting.
*Scientists also used to E. coli levels to infer the risk of contracting campylobacteriosis, a common disease in New Zealand. Campylobacter, its pathogen, is one of the most common pathogens associated with faeces in New Zealand, but is more difficult and costly to measure than E. coli.
By the numbers
•An analysis of 928 spots tested between 2009 and 2013 for E.coli showed that all urban sites exceeded the minimum acceptable state for "primary contact" like swimming, as set out by the Government's National Policy Statement for Freshwater Management.
•This threshold was also crossed at 91 per cent of pastoral sites, 46 per cent of exotic forest sites and 29 per cent of "natural" areas of native forest.
•About half of New Zealand's river length is fed by catchments that are mainly influenced by indigenous land cover, while 45.7 percent are influenced mainly by pasture, 5.1 percent by exotic forest, and 0.8 percent by urban land cover.
