The Department of Environment and Science has confirmed it will investigate Adani after water from the north Queensland floods spilt from the Abbot Point coal port last week into wetlands.
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The department's test results came back on Wednesday and showed the level of "total suspended solids" - the volume of debris such as soil, plant material or dust - in the water was 33mg/L.
Adani said on Tuesday the level of total suspended solids was 58mg/L, according to the separate test it commissioned. The authorised maximum level according to the company's licence is only 30mg/L.
Adani did not apply for a temporary licence to exceed its total suspended solids limit.
The environment department said the potential reason for the difference in debris levels was because the department's sample was collected on Friday and Adani collected its sample on Thursday.
"A copy of the results from DES sampling has been provided to the coal terminal operators – Abbot Point Bulk Coal Pty Ltd," the department said in a statement on Wednesday afternoon.
"An investigation into the alleged non-compliance has commenced in accordance with the department’s standard procedures.
"DES will now issue the coal terminal operator with a show cause letter inviting the company to make representations as to why enforcement action should not be taken."
The mining company confirmed in a statement on Tuesday the water reached the nearby 5000-hectare Caley Valley Wetlands but did not flow into the Great Barrier Reef Marine Park.
The potential environmental threat could come from coal "fines" - small coal particles - which were in the Abbot Point port water and might have been washed into the wetlands.
Abbot Point Operations chief executive Dwayne Freeman said the water was not "coal-laden sludge" and described the spike in total suspended solids as a "very minor elevation".
"We are confident there will be no environmental impacts to the wetlands area, despite this unprecedented weather event," he said.
"Normally a company would not release its test results, but we recognise there is a high level of public interest in Abbot Point terminal’s operations.
"As a result of this, we are releasing these results in an effort to keep the community informed and to demonstrate our commitment to operating transparently and with integrity."
Mr Freeman said the coal terminal received more than 900mm of rain since December and the monsoonal rain, responsible for the Townsville and north-west Queensland flood disasters, led to the site not being able to handle the water any more.
"The weather has been extreme up here at Abbot Point. Heavy rainfall has seen a significant amount of water accumulating on the port site and surrounding properties,'' he said.
"The floodwater from our neighbouring properties on Thursday, February 7, could not be contained any longer and exceeded our systems' capacity, resulting in floodwater entering the wetlands.''
The Abbot Point Terminal has been completing more than $15 million in upgrades, which includes increasing the volume of water storage ponds as well as new piping and pump facilities.
The port was closed early last week because of the torrential downpour and when staff returned on Thursday they find the port had overflowed into the adjacent wetlands.
The Caley Valley Wetlands are an important coastal conservation region home to many wading birds, swans, sea eagles and wildflowers.
