UNESCO has warned that without action on water quality and rampant coastal development the reef - covering an area roughly the size of Japan - would be declared "World Heritage in Danger".
Queensland state Environment Minister Andrew Powell said progress had been made as he released a government report card on action taken to improve water quality since 2009.
"I do not expect that will happen," he said of a potential UN downgrade.
The report, which Powell will take to a UNESCO meeting in Doha later this month, shows reductions in key pollutants, including sediments and pesticide run-offs on the back of improved land management practices.
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"Pesticide loads, we have reduced it by 28 per cent across the whole reef catchment," Powell said.
"In terms of nitrogen - that's what causes those crown-of-thorn starfish outbreaks - we have reduced it by 16 per cent overall."
But while improvements to water quality had been achieved, Powell conceded that the overall health of the reef still needed more work.
The report dealt only with water quality issues and not port developments linked to mining, which conservationists have warned could hasten the demise of the reef.
There has been particular concern about the government in December approving a massive coal port expansion in the region and allowing the dumping of up to three million cubic metres of dredge waste within the marine park waters.
Powell insisted to ABC radio that port development was not the main threat to the reef, one of the most biodiverse places on Earth.