The decision in January to allow three million cubic metres of dredge waste to be disposed of in park waters followed a decision by the government to give the green light to a major coal port expansion for India's Adani Group on the reef coast in December.
Conservationists warn it could hasten the demise of the reef, which is already considered to be in "poor" health, with dredging smothering corals and seagrasses and exposing them to poisons and elevated levels of nutrients.
It asked the government to provide a new report to the World Heritage Committee proving that dumping was the least damaging option and would not hurt the reef's value.
More generally, UNESCO expressed concern "regarding serious decline in the condition of the Great Barrier Reef, including in coral recruitment and reef-building across extensive parts of the property".
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The body said "a business-as-usual approach to managing the property is not an option".
WWF Australia spokesman Richard Leck said the government needed to act quickly to prevent the embarrassment of the reef being listed as in danger.
"UNESCO'S concern is shared by thousands of Australians and hundreds of leading scientists and we call on the federal government to ban dumping of dredge spoil in the Great Barrier Reef World Heritage Area prior to the World Heritage Committee meeting in June," he said.
The government in February insisted it had made "substantial" progress on UNESCO benchmarks for protection of the reef in a report aimed at staving off a world heritage downgrade.
According to the report, Australia was taking steps to bolster the reef's resilience to the major threats of extreme weather events and climate change, which it said "cannot be managed directly".