A report from Queensland's auditor-general has questioned the State Government's claim that water quality on the Great Barrier Reef is improving.

The auditor-general's report examines the Queensland Government's handling of agricultural run-off from farms over the last 12 years.

It found the State Government's response has been uncoordinated, lacks purpose, and holds no-one accountable.

The auditor-general's report said Queensland was yet to design a program for its contribution to the Reef Plan, which was developed 12 years ago.

It said a 2014 reef report card's claims the decline in water quality had been reversed was not necessarily true.

In his recommendations, auditor-general Andrew Greaves said there was a need for more stringent monitoring on farms and the suite of water quality programs must be reviewed to ensure they were working.

The report also called for the new Office of the Great Barrier Reef to be held accountable for the health of the reef.

Public reporting misleading at worst: A-G report

WWF-Australia said in a statement the auditor-general's report exposed government failures that resulted in the Australian people and Unesco being misled on the Great Barrier Reef.

It said "for the last few years government reef report cards have told Australians and Unesco that pollution levels were improving".

In the report, Mr Greaves found these report cards of improvements could not be relied on as fact.

"The regular public reporting fails in this regard, lacking transparency at best, and being misleading at worst," the report said.

WWF-Australia CEO Dermot O'Gorman said the auditor-general's report clearly validated "Unesco's latest decision on the reef that puts Australia on probation until real results are achieved including actual reductions in pollution levels".

"Given the auditor-general's findings on the high level of uncertainty, it would be wrong to continue to quote these as reef facts," Mr O'Gorman said.

"Governments must ensure that under the Reef 2050 plan they guarantee that the reporting system for pollution flowing to the reef will be completely independent, with all data released immediately each year, and regulations enforced to stem pollution.

"WWF calls on the government to fully implement the auditor-general's recommendations."

Premier Annastacia Palaszczuk said she was taking action.

"My Government is committed to spending $100 million in improving the water quality of the Great Barrier Reef [and] also stopping the capital dredge spoil being dumped into the World Heritage area," she said.

Successive governments have been trying to control nutrient and sediment run-off that diminishes water quality and boosts the numbers of crown of thorns starfish – one of the biggest risks to the reef.

In March, the federal and Queensland governments released a long-term plan for the Great Barrier Reef.

The Reef 2050 Long-Term Sustainability Plan satisfied one of the key recommendations made by the World Heritage Committee and formed a key plank in the governments' bid to avoid the site being declared "in danger" by Unesco.

Previously, a draft version of the report was criticised by some scientists as being a plan for sustainable development rather than protecting and conserving the reef.

The Queensland Government also sought urgent changes to that draft to include its $100 million election commitment to improve water quality.

In May, Unesco recommended that the Great Barrier Reef not be placed on the World Heritage "in danger" list.