The new report, also backed by the Public Health Association, notes contaminated water increases the risk of acute illnesses from pathogens - and links high livestock density to increases in reported disease.
"The Public Health Association is very concerned that unless there are changes to the way we farm, New Zealanders will be facing more illness and deaths caused by contaminated water," PHA chief executive Warren Lindberg said.
"Maintaining the status quo is not an option, let alone encouraging the increase in livestock numbers by investing in more irrigation schemes.
"We must act immediately to reduce livestock numbers and ensure the safety of our water supplies to protect public health."
Canterbury Medical Officer of Health and GP Dr Alistair Humphrey also contributed to the report, criticising a "relentless" growth in intensified dairying.
The report noted good work by farmers to clean up pollution but added this would be undermined by Government-supported plans for dairy expansion, with $480 million ear-marked to build irrigation schemes.
"A precautionary approach would see health warnings heeded rather than millions of taxpayer dollars spent on irrigation schemes," the report stated.
It recommended a new low-input ecological model of farming, involving fewer cows per hectare and no nitrogen fertiliser.
Greenpeace spokeswoman Amanda Larsson said scientists estimate contaminated water causes between 18,000 and 34,000 cases of gastrointestinal illness in New Zealand each year.
"Where there is clear evidence of potential risk to human health, the Government has a responsibility to take the precautionary approach," she said.
"But right now, it's doing the opposite."
A spokesperson for Environment Minister Nick Smith referred questions to Primary Industries Minister Nathan Guy, who has been approached for comment.
Federated Farmers water spokesperson Chris Allen said farmers were already doing a "huge amount" to reduce their environmental footprint.
Allen said farmers operated under the Resource Management Act, which involved managing effects rather than cutting input.
He also argued irrigation played a big part in managing nutrients more effectively.
Allen added farmers were "absolutely over" being blamed for waterway pollution -
higher levels of freshwater contamination came from urban sources - and argued the sector had "stepped up to the mark" to address the issue.
The Government's Clean Water Package includes a target that 90 per cent of New Zealand's rivers and lakes are swimmable by 2040, with an interim target of 80 per cent by 2030.
It also included better information on water quality for swimming, proposals for changes to the National Policy Statement for Freshwater Management 2014, details of proposals to exclude stock from waterways, and the $100 million Freshwater Improvement Fund.
State of our rivers: What the figures show
• A recent Government stocktake showed E.coli concentration was 22 times higher in urban areas and 9.5 times higher in the pastoral areas compared with native land. Of 268 river sites in pastoral areas monitored between 2004 and 2013, E.coli trends were "indeterminate" at 65 per cent, improving at 21 per cent, and worsening at 14 per cent of sites.
• Levels of nitrate-nitrogen in monitored rivers was worsening (55 per cent) at more sites than improving (28 per cent), and dissolved reactive phosphorus was improving (42 per cent) at more sites than worsening (25 per cent) between 1994 and 2013. Between 2009 and 2013, concentrations of nitrate-nitrogen concentration were 18 times higher in the urban areas, and 10 times higher in the pastoral areas.
• Of 175 monitored river sites in pastoral areas, nitrate-nitrogen trends were worsening at 61 per cent and improving at 22 per cent of sites for the period 1994 to 2013 period. Nitrogen leaching from agricultural soils was estimated to have increased 29 per cent from 1990 to 2012.
• Virtually all of New Zealand's total river length - more than 99 per cent - was estimated not to have nitrate-nitrogen concentrations high enough to affect the growth of multiple sensitive freshwater species for the 2009-13 period. In the same period, dissolved reactive phosphorus concentration was three times higher in the urban areas, and 2.5 times higher in the pastoral areas, compared with the native land.
• Of 145 monitored river sites in pastoral areas, trends in dissolved reactive phosphorus were improving at 46 per cent and worsening at 21 per cent of sites between 1994 and 2013.
