Australia's environment minister Sussan Ley said Canberra would challenge the recommendation, saying it went against advice given just a week ago, and defended Australia's protection of the reef.
"This is a complete subversion of normal process," Ley said.
Australia has for years been battling to keep the Great Barrier Reef, a major tourist attraction that supports thousands of jobs, off the "in danger" list, a step that could potentially lead towards its eventual removal as a World Heritage Site.
Ley said she and Australia's minister for foreign affairs Marise Payne raised their concerns overnight with the director general of UNESCO, Audrey Azoulay.
A government source said Canberra believes China, which chairs the committee, is responsible for the move amid a souring of relations between the two countries.
China's embassy in Canberra did not immediately respond to a request for comment.
Environmental groups, however, rejected that the recommendation was political and said it was clear Australia was not doing enough to protect the reef, especially on climate change.
"There is no avenue for any government to have any input. This recommendation is reached by world renowned scientists," said Richard Leck, head of Oceans for the World Wide Fund for Nature, Australia.
Leck was part of a group of conservationists that lobbied 13 members of the UNESCO committee to reach its recommendation, which will now be considered by all 21 countries on the committee.