Coal dust has spread throughout the Great Barrier Reef and exceeds toxic levels near the shore, a Senate inquiry has heard.

Senators are touring Queensland this week to examine how the Australian and Queensland governments manage the reef, as UNESCO threatens to list it as a World Heritage site in danger.

James Cook University (JCU) Professor Terry Hughes says a "damning" new report from the university shows coastal sediments offshore of the Hay Point coal port are contaminated with coal residues that exceed Australian guidelines.

Prof Hughes, who is also the director of the Australian Research Council Centre of Excellence for Coral Reef Studies, said the report also found coal dust had spread hundreds of kilometres from ports.

"It has now accumulated everywhere on the Great Barrier Reef, not just near dredging sites or near the ports themselves and it is exceeding toxic levels in near-shore locations," he told the inquiry, which sat in Townsville on Wednesday.