Carmichael coal mine operator Bravus must do further groundwater modelling if it wants to proceed with underground operations that could impact the sacred site of Doongmabulla springs.
The company formally known as Adani performs open-cut mining at the central Queensland site, and admits it has "additional work to do" on future underground plans.
It has been issued with an environmental protection order by the Queensland Environment Department following a groundwater model report on predicted impacts if underground mining commences as planned post 2034.
Based on a preliminary review, the report indicates no predicted impacts to the springs from current and future open cut mining, the department said in a statement on Friday.
"However, the report indicates there may be impacts to the springs from future underground mining under the current approved mine plan," it says.
"It demonstrates underground operations will result in a predicted drawdown which is not consistent with approved impacts."
An Environmental Protection Order has been issued, requiring Bravus to undertake a second groundwater model "re-run" and not to commence underground mining until it gets approval from the department.
"The department recognises the significant cultural and environmental values attached to the Doongmabulla Springs Complex and is committed to ensuring the highest protection is afforded to the springs," it says.
But environmental groups are worried the report confirms "what we've always feared".
"This research on the risks to the springs should have been done many years ago, and it's appalling that Queensland and Federal governments both approved the mine without properly understanding the threats to this extraordinary spring system," Lock the Gate Alliance National Coordinator Ellen Roberts said in a statement on Friday.
The mine's environmental authority was designed on an "adaptive management" approach, meaning regular re-runs of the original modelling are required using data collected since mining began.
The groundwater model uses data recorded every two months from a network of about 120 bores on and around Bravus' mining and pastoral leases.
Surface water samples are collected from another 15 locations including the Doongmabulla springs complex, which is a grouping of individual springs that discharge water from the Great Artesian Basin, the company said in a statement on Wednesday.
The nearest of the springs is located about 11 kilometres from mine activity at Carmichael.
""While we are not doing any underground mining now, the new model does indicate we have additional work to do on our future underground mining plans to ensure they do not cause water levels in the springs to fall by more than the 20 centimetres after mining occurs, which is one of our regulatory conditions," Bravus Mining and Resources Chief Operating Officer Mick Crowe said.
""Protecting the springs has always been a top priority for us as we understand both their value to the Traditional Owners of the area and their inherent environmental value, and we will now use the science and the model to rework our future underground mining plans to ensure we comply with our approvals."