One of the most contentious conditions imposed by the federal government on the project is the need to ensure that rail loop impacts from earthworks run off, including impacts on the Great Barrier Reef and on marine species, are mitigated, particularly in relation to the potential impacts on the near-shore habitat for dugongs, turtles and dolphins.

Burke is under pressure to deny approval of key coal terminals in north Queensland after UNESCO called for a strategic assessment before considering future coastal development as well as an independent review of the port of Gladstone.

It warned the government to improve conservation efforts by February to avoid placing the reef “in danger”

“On Thursday 7 June, I met with Queensland Deputy Premier Seeney and Queensland Environment Minister Powell, to discuss concerns about the way the project had been assessed by the Queensland coordinator general under the joint bilateral arrangement,” Burke said.

“It was agreed at that meeting that my department would conduct a separate national environmental assessment process for Alpha Coal mine and rail project.

“In doing so, my department have stopped the clock on the approval timeline whilst it seeks further information from the company.

“Stopping the clock does not mean stopping the process. In fact the process has progressed significantly during this recent period.

“This is a common practice to ensure my department has all the necessary information for a fully-informed decision. Once this additional information is provided, the clock will be restarted and a new statutory deadline will be set.

“My department has met with the proponent twice, on the 5th of June and again yesterday to obtain further information on their proposal.”

Burke also called for the need for more work on species habitat modelling and surveys to ensure the impacts on matters of national environmental significance, including listed migratory species in the Caley Valley Wetlands and listed threatened species and ecological communities.

He also asked Hancock-GVK to clarify the way the company’s cumulative impacts studies on Abbot Point interacted with other cumulative impact studies on the port and the need for an enhanced “like-for-like” offsets package.

The changes to the existing bilateral agreement for environmental approvals for major projects were a major step forward and introduced project management approaches to the process, Seeney said.

They also gave greater clarity and transparency about the respective roles of the state and federal governments and imposed timeframes on both for consultation and responses through the approvals process, he said.

The new agreement includes the setting of defined milestones and timeframes for providing documents, feedback and approvals, including the signing-off on terms of reference and key assessment reports.

Seeney said the new bilateral agreement would eliminate duplication in the environmental approval process which in the past had bogged down some projects for years.

"The changes negotiated between the state and Commonwealth will also provide certainty to project proponents around the length of time of the approval process," he said.

"This is a clear step forward which will enable Queensland to get on with the job and deliver the best environmental and economic outcomes for this state.

Minister for Environment and Heritage Protection Andrew Powell said the signing was a positive outcome for Queensland and consistent with the LNP's election commitment to reduce green tape.

"Our position throughout this discussion has been consistent. There has been a lack of clarity around what is expected from all parties with regards to these agreements. The changes to this bilateral agreement address these," Powell said.

Powell said the federal and state governments were committed to maintaining the highest environmental standards while at the same time streamlining the environmental assessment and approval process.