A $261 million Queensland Government water quality program is failing to protect the Great Barrier Reef from fertiliser run-off, with sugar cane farmers still using excessive chemicals on their properties, Right to Information (RTI) documents obtained by the ABC reveal.

Key points: Forty-nine per cent of audited sugar cane farming businesses were not complying with the law

Forty-nine per cent of audited sugar cane farming businesses were not complying with the law No farmer has faced prosecution

No farmer has faced prosecution Scientists say there is no evidence voluntary measures are improving water quality

In 2009, the Queensland Government passed a law setting "the optimum amount" of fertiliser farmers are allowed to use.

But the documents show widespread overuse of nitrogen and phosphorous, although there is no evidence any farmer has ever been prosecuted and faced the fines of up to $10,000.

The RTI documents, which deal with the financial year to the end of June, indicate that no farmers have been prosecuted.

When asked about prosecutions by the ABC in March this year, a Department of Environment and Science (DES) spokesperson said that: "To date, no growers have been prosecuted for contraventions of Chapter 4A of the Environmental Protection Act 1994".

The ABC has since contacted the DES again to inquire whether any growers have been prosecuted since then.

The law applies to three "priority catchments" — Mackay-Whitsundays, Burdekin and Wet Tropics — but the Government has considered broadening the legislation to include Cape York, Fitzroy and Burnett Mary regions.

Government audits of 344 sugar cane farming businesses in 2017-18 in the three "priority" areas showed 49 per cent were not complying with the law. The rest were either compliant, under assessment, had stopped farming or were engaged in other water quality improvement programs.

Even after further inspections, 43 per cent of farm businesses still failed to abide by the law.

The State Government documents show that in 2016-17, only 14 per cent of audited farm businesses were compliant, falling to 7 per cent last financial year.

The documents show the main reason for non-compliance in the three audited areas was cane farming businesses using too much nitrogen. Other reasons for non-compliance were failure to test the soil, inadequate record-keeping and using too much phosphorous.

When nitrogen hits the reef, it leads to algal blooms, providing food for juvenile crown-of-thorns starfish, which eat coral when they reach adulthood.

The DES documents note: "The main source of the primary reef pollutants (nutrients, fine sediments and pesticides) from GBR catchments is diffuse source pollution from agriculture."

No farmer has ever been prosecuted for contraventions of Chapter 4A. ( ABC News: Marty McCarthy )

'No sign water quality is improving'

Rather than enforcing the existing law, the State Government has let the industry change its practices through a voluntary program called best management practices (BMP). It has allocated more than one-fifth of the $261.08 million funding to BMP.

"In 2012, Reef Regulations were put aside in favour of industry-led voluntary BMP programs to allow the industry to encourage and drive improved practices in sugar cane production," the DES spokesperson said.

The program helps farmers identify how much fertiliser they can apply in order to fit within legal limits. Upon completion, farmers become accredited and are assumed to be using the allowed amount of fertiliser.

Two days after the ABC obtained the RTI documents, the Minister for the Great Barrier Reef, Leeanne Enoch, announced an additional $6 million funding to boost BMP.

BMP-accredited farmers are asked to provide records of their fertiliser use to industry consultants but are not physically inspected by Government compliance officers because they are considered to be at "low risk of non-compliance".

The industry peak body, Canegrowers, said 9 per cent of all 3,500 farm businesses across the state were accredited — up 3 per cent from last year — but that 71 per cent of land under cane was run by farm businesses that were "involved in the program" but had not completed it.

Dr Jon Brodie says "there is no sign really" the water quality is improving. ( ABC News: Laura Hegarty )

Dr Jon Brodie from James Cook University's coral reef studies department said even though most of the sugar cane land is said to be managed by farmers who monitor their water quality, scientists had not noticed improvements.

"We've been monitoring water quality both in rivers, streams, off the end of farms and in the marine environment, and at the moment there's no sign really that the water quality is improving," he said.

"The other thing to think about is that we've now spent $1 billion on [water quality] programs over the last 10 years and yet the results, according to the official Government report, are quite poor."

The ABC spoke to a former Canegrowers' employee, Simon (not his real name), on the condition of anonymity.

He said without Government officials testing water quality on BMP-accredited farms it was difficult to prove growers following the program were applying legal amounts of fertilisers, and whether applying BMP really resulted in water quality changes.

"I don't think there's any way to verify that [farmers] are following them," he said.

"I don't think it's been proven that [BMP] have real water quality benefits."

The DES spokesperson told the ABC the BMP were "based on rigorous evidence and science" and said the uptake had been "good".

But the RTI documents show last financial year, only 9 per cent of 344 audited farm businesses contacted by Government's compliance officers were marked as using BMP, and 25 per cent as engaging in other practice-change programs. This compares to the year before when 18 per cent of farms used BMP and 17 per cent other programs.

The documents show the State Government knows "despite significant investment and goodwill from all parties, not enough has been achieved and accelerated uptake of improved practices is urgently needed to achieve the water quality targets".

'Hundreds of scientists' say fertiliser overuse an issue

Nitrogen run-off from sugar cane farms is one of the main threats to the Great Barrier Reef. Nitrogen encourages the growth of algae, which is a source of food for juvenile crown-of-thorns starfish. When the starfish reach adulthood they feed on coral, killing it.

"These starfish, when they're adults, eat through huge areas of coral, and have been responsible for significant [coral cover] losses over the last three decades," WWF's reef and water manager Sean Hoobin said.

Dr Brodie said "hundreds of scientists" agreed fertiliser over-use was contributing to the decline of the reef, and the industry was aware of it.

"We've been talking to cane farmers for many, many years — decades, in fact — about how run-off of nutrients affects the Great Barrier Reef, and specifically about how run-off from extra nitrates from sugar cane fertiliser affects the Great Barrier Reef," he said.

Crown-of-thorns starfish feed on coral, killing it. ( Flickr: Ryan McMinds )

'Reluctance to enforce regulations'

The Queensland Government has been promoting BMP as an alternative to regulating the industry since 2012.

But Mr Hoobin said the uptake had been "so low" the argument existing laws should not be enforced was "completely flawed".

"I'm almost scared to think how much illegal pollution has been dumped on the reef because the Government hasn't enforced its own laws," he said.

"Hundreds of millions of dollars are going into [tackling] the pollution going into the reef but unless the Government enforces these pollution laws, that money is being wasted."

Sean Hoobin says "illegal pollution has been dumped on the reef". ( Supplied: WWF )

Industry worker Tina (not her real name), said the decision not to enforce the laws was politically motivated.

"You can't be seen to be damaging the industry. Any risk to growing less cane isn't acceptable. There's a lot of money in mills and they want cane going through them," she said.

Dr Evan Hamman from the Queensland University of Technology has been researching the application of laws in the sugar cane industry.

He also questioned why the laws that were "actually not bad on the books" had never been enforced.

"There's definitely something going on there with the reluctance to enforce regulations and going down the path of non-regulatory approaches," he said.

Asked if failing to comply with the law constituted engaging in illegal activities, Canegrowers chairman Paul Schembri said that was for the Government to decide.

"Well, obviously if a law is written there is a certain threshold test that applies when somebody is seen to be breaking the law, but I don't administer the law in relation to these regulations. It's a matter for the Government," he said.

The State Government has been promoting BMP as an alternative to regulating the industry. ( ABC Far North: Mark Rigby )

'There obviously is an issue': farmer

Cane grower Ray Zamora from the Tully River catchment in the Wet Tropics said "there obviously is an issue with nitrogen running off to the reef".

The BMP-accredited farmer said he had reduced nitrogen levels for his crops, but not everyone "worried about" changing their practices.

"Yes, there's possibly some people out there that wouldn't be doing the correct things. I think we just need to prove to them that they can use a little bit less nitrogen and get the same, if not a better, result for both their economics and their environment," he said.

Canegrowers senior vice-chairman Allan Dingle said the industry was "doing everything it can" to control nitrogen run-off, and should not be regulated.

"I think you'll get a far better outcome by letting the industry try and manage the process itself, and we're attempting to do that through BMP," he said.

"We think that although the uptake in some people's eyes has been slow, you compare it to other industries, we're probably doing quite sweetly."

But Dr Brodie said time was running out for the reef.

"The story is just disastrous really. It's very sad. The only advice I have for younger people is, if you want to see the Great Barrier Reef in some sort of reasonable state, go now — don't wait," he said.