Excluding cattle from access to waterways helps maintain water quality and prevent effluent pollution.
The number of dairy farms that completely prevent stock access to waterways has been surveyed by the Ministry of Agriculture and Forestry, with results showing much less compliance than previous findings.
The independent survey, released on Tuesday, found only 42.1 per cent of farms nationally had achieved complete stock exclusion, with a margin of error of 4 per cent.
Previous figures released by Fonterra put complete stock exclusion at 84 per cent.
The survey was commissioned by MAF to assess the progress of dairy farmers towards achieving the Dairying and Clean Streams Accord target that dairy cattle are to be excluded from 90 per cent of streams, rivers and lakes by 2012.
Excluding cattle from access to waterways helps maintain water quality and prevent effluent pollution.
Fish and Game New Zealand claims the discrepancy comes from the fact Fonterra uses self survey methods.
"Fish & Game has constantly highlighted the problem of the dairy industry self-reporting and we've repeatedly questioned the 'success' of the Accord when the science clearly tells us water quality in most regions is still declining," Fish and Game chief executive Bryce Johnson said.
Fonterra's results came from interviewing farmers and asking them a range of questions about their farm practices, as opposed to the MAF survey which used a technician to visually assess a sample of randomly selected farms.
"While Fonterra's survey of farmers suggests 84 per cent of properties have stock excluded from waterways, the reality is only half that number of farms nationally have complete stock exclusion - that's clearly what MAF's independent audit reveals," Mr Johnson said.
Fonterra's general manager milk supply Steve Murphy said the survey results were mixed.
"Overall, it highlights that a lot of progress has been made by farmers but, ultimately, we recognise that there is still more that needs to be done," he said.
In a step to curb the problem, Fonterra recently announced that it would include stock exclusion from Accord-type waterways as a condition of supply from the start of the 2012-13 season.
Suppliers will have until June 2013 to complete exclusion work.
The MAF survey identified Hawke's Bay as the third best placed region, with 57 per cent compliance. In first and second places were Canterbury (65 per cent), followed by Southland (60 per cent).