One of the world's premier coral reef research centres has failed to secure Australian Research Council funding, placing in doubt the science hub even as the Great Barrier Reef faces another bout of bleaching.

The council confirmed in Senate estimate on Thursday that the Townsville-based Centre of Excellence for Coral Reef Studies missed out on even making the funding shortlist for its next round of funding.

Professor Terry Hughes, head of the ARC Centre of Excellence for Coral Science Studies, James Cook University, has often been critical of government policy. Credit:James South

"It's certainly an esteemed centre," Professor Sue Thomas, the council's chief executive, told estimates.

She rejected criticism from Labor's science spokesman, Kim Carr, that the centre's missing out was the result of "political intervention" because of outspoken criticism from its head Terry Hughes of the government's reef policy.