KAP deputy leader Nick Dametto's bill had sought wind back the Labor government's 2019 reef protections which penalised landholders over sediment runoff into the reef.

Mr Dametto warned the continuation of existing reef regulations could cripple the sugar cane industry in the north Queensland.

"There is a widespread fear throughout our cane communities that history will show the reef regulations to be the catalyst that will slowly shut down the industry," he said on Wednesday.

The state's peak cane, cattle, grains, sheep and wool producers' body AgForce slammed the major parties for voting down the crossbench party's bill on Tuesday night.

AgForce's reef taskforce chair Alex Stubbs said with state politicians unwilling change runoff laws, the only way to deal with it was a new national auditor to check the science behind reef regulations.

"When our calls are finally answered we can prove once and for all that land-based runoff of fertilisers and pesticides is not harming the reef, and that the current level of regulation is a hindrance and not a help," he said.

Mr Stubbs said the defeat of the bill is deeply disappointing as it would mean a continuation of onerous and unfair regulations for producers.

"This would most certainly have been a step in the right direction for reef regulations," he said.

"Ultimately, why regulate pesticide usage across reef catchments, when water quality monitoring shows detected levels in river deltas are not above water quality trigger values.

"Why impose cane farm budgets for fertiliser use when the latest science has shown many factors cause crowns-of-thorns outbreaks and that there is no proof that fertiliser runoff is linked to this.

"By wrongly targeting the farming community, the state government is simply failing to protect the reef."

Mr Stubbs said the Great Barrier Reef Marine Park Authority had said the biggest threats to the reef are rising ocean temperatures due to climate change, damaging tropical cyclones, and crown-of-thorns starfish outbreaks.

Greens MP Amy MacMahon didn't support bill, pointing out GBRMPA said in 2019 that land based sediment and nutrient runoff were one of the biggest threats to the reef.

However, she said farmers were right to feel hard done by the state government as it was forcing them to do the "heavy lifting" without acting itself against climate change.

"Farmers are on the front lines of climate change and, if we did climate action right, climate action would include support and improved prosperity for farmers who care for the land every day," Ms MacMahon told parliament on Tuesday.

Australian Associated Press