A freshwater ecologist is accusing the dairy industry of propagating spin.

It follows a new report that claims 97 percent of our waterways are now fenced-off from dairy cattle - a claim Massey University senior lecturer Mike Joy rejects.

Mr Joy says dairy is on the charm offensive. He told Mike Hosking only a fraction of our waterways are covered in the report.

"I would guess that overall, it's probably 97 percent of 50 percent of our waterways," he said.

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"To claim 97 percent of waterways but not mention that it's what you define as a waterway, that's wrong.

"All of the small streams that feed into those larger streams don't have fences. All of the rubbish can get in, all of the pathogens that make people sick can get in from those smaller ones. If you don't get them all, then you don't deal with the problem."

Forest & Bird says efforts by farmers to protect our waterways aren't up to scratch.

Advocacy manager Kevin Hackwell told Rachel Smalley some farmers still aren't pulling their weight.

"Yes, they've fenced an awful lot of the streams, but those are the biggest streams, what about the smaller ones where actually most of the pollution enters."

Hackwell said all regionally significant wetlands have yet to be fenced-off.

"100 percent of them should have been fenced by 2014. They were meant to have fenced them and they haven't."