Scientists and government science agencies have found themselves at loggerheads with Queensland cane growers over water quality in the reef, and they're not hiding from the fight.

"The Australian Academy of Science is greatly concerned about a recent tendency to cherry pick, dismiss, misrepresent, or obscure scientific evidence or smear individual scientists," president Professor John Shine said.

"Cherry-picking evidence to support a decision or position is dangerous and leads to poor judgement and outcomes."

His comments are in a submission to a parliamentary inquiry that is examining the science behind the decision to limit farm run-off into the reef. The inquiry was set up by the Nationals and Liberals, and strongly supported by One Nation, which congratulated renegade scientist Peter Ridd for rubbishing the science and supporting the farmers.

Dr Ridd says claims about "supposed threats" from farm run-off are "even less convincing and more contrived" than claims about climate change.

But Prof Shine said the science behind the decision to limit run-off was established.

The 2017 Scientific Consensus Statement had 11 main authors and 38 contributing authors, including scientists from government, private sector and research agencies. In 2019, the Great Barrier Reef Outlook Report collected decades of research from hundreds, perhaps thousands, of scientists, he said.

In August, the government's independent expert panel on the reef, chaired by former chief scientist Ian Chubb was spurred into action by what it termed Dr Ridd's "roadshow". In a letter to federal and state ministers, it said it would not "sit by and watch the science being disputed and misrepresented". Global warming from human activity was the biggest reef risk, and poor water quality from nutrients, sediments and pesticides flowing to the sea was a major threat, it said.

The inquiry received more than 40 submissions, including from the federal government's own environment department and from the CSIRO. Both stressed the exhaustive and extensive science on the reef over more than two decades.

The environment department said plans to improve water quality were unpinned by the best available science, including more than 1600 papers and reports reviewed for the Scientific Consensus Statement.

It found that nutrients stressed corals and promoted crown-of-thorns starfish outbreaks, fine sediments reduced light to seagrass and reefs, and pesticides were toxic.

The water quality 2050 plan aimed for a 60 per cent reduction in nitrogen, a 25 per cent reduction in sediment, and a 20 per cent reduction nutrient loads, it said.

But Bundaberg Canegrowers manager Dale Holliss said the group did not accept the science without question, and $5 million of reef money should be set aside for an "Institute of Policy Science Quality Control" to monitor reef science.

Proserpine Canegrowers manager Michael Porter said the science was subjective and dangerously unproven and the canegrowers were infuriated by the unattainable water quality targets.

Australian Cane Farmers manager Stephen Ryan called for water quality data to be made available to farmers with help to interpret it.

"Continual water monitoring, especially real-time, in-stream monitoring, would provide a clearer picture of the effect of farms on water quality. This would help to overcome farmers' concerns and perceptions about the timing of intermittent sampling by government departments," he said.

Jennifer Marohasy, a well-known climate sceptic accused governments of deliberately hiding water data it to "maintain the perception of declining water quality, while in reality, the situation is improving".