An investigation into Adani's Abbot Point Terminal in north Queensland has been launched to determine if it made unauthorised water releases into nearby wetlands.
A spokeswoman for the Department of Environment and Heritage Protection says it has started an inquiry after satellite images appeared to show "sediment-laden water" flowing into Caley Valley.
She said the Indian mining and energy company had applied for and been granted a temporary emissions licence (TEL) during Cyclone Debbie, which relaxed or modified its operating conditions.
"A TEL does not authorise environmental harm," she said in a statement on Monday.
She said Adani was granted the licence to assist it with its water management at the Abbot Point facility during the cyclone.
"The TEL permitted a temporary increase to the release limits for total suspended solids from 30mg/L to 100mg/L," she said.
"By comparison, the total suspended solids in central Queensland waterways following rainfall events typically exceed 1000mg/L."
Construction on Adani's $21.7 billion project, to build Australia's largest coal mine in the Galilee Basin and connect it to Abbot Point via a 31.5-kilometre rail line, is expected to start next year.
The departmental spokeswoman said "initial monitoring results" showed the water releases into the wetlands were in accordance with the temporary licence.
"EHP's investigation is continuing, including accessing historical satellite imagery to compare wetland colour and depth fluctuations," she said.
Adani has been contacted for comment.
