While it admits Alpha North would impact threatened species including koalas and the Curlew Sandpiper, Waratah claims it can safely work around critically endangered wildlife.
The company has not yet provided an up to date environmental assessment for the project.
The Alpha North project is planned to consist of two open cut operations and four underground longwall mining operations, coal handling preparation plants and a rail spur transportation network to the Galilee Coal Project rail network.
The project intends to mine 56 million tonnes per annum of run-of-mine coal, which will be later processed to produce 40Mtpa of product coal.
The project is proposed to begin operations with a 10Mtpa open cut mine, eventually ramping up to 56Mtpa several years later.
Opponents of Alpha North claim the project would account for 31% of Australia's domestic greenhouse gas emissions.
"To submit an application for a coal mine three times larger than Adani's controversial Carmichael mine without doing any environmental assessment is like expecting to get a physics degree just by turning up on graduation day," Greenpeace Australia Pacific Campaigner Jonathan Moylan said.
"This is a message from Clive Palmer to the environment department that the coal industry considers them to be a rubber stamp."
Moylan said Waratah had failed to acknowledge any impacts on national parks and underground water systems that were vital for agriculture as well as biodiversity.