The information was gleaned from a report on water quality at the site calling for farmers to be more careful with their chemicals, the BBC reported.
The report said about 25 percent of horticulture producers and more than 10 percent of farmers were using practices unacceptable to the industry.
The Great Barrier Reef is a World Heritage-listed natural wonder. The Australian report said the sugar cane industry in the wet tropics of northern Queensland is a major polluter.
Investigators said Cyclone Yasi flushed some of the pollutants into the ocean, but many horticulture producers were still using methods considered unacceptable. Chemicals were found in waters nearly 40 miles from shore, the report said.
Conservationists have called on farmers to limit the use of pesticides and to ban some weed killers. Sugar cane producers said there are no alternatives if they're to protect their crops.