Satellite images from 2021 reveal hundreds of hectares of land at Claravale Station was cleared without a permit.
The images, uncovered in an ABC investigation, show land cleared closer than permitted to the Daly River.
A clearing permit was issued for part of the razed land in September 2021, while the federal government later announced an investigation which is yet to make any findings.
In a leaked letter seen by AAP on Monday, NT Infrastructure Minister Joel Bowden confirmed the territory government filed criminal charges against the station in November.
"(I) determined to prosecute the matter … under the Planning Act" Mr Bowden wrote.
He said on Monday that some work had been undertaken before an application was processed.
"There was an application made, unfortunately, what was found was that there was some work being done prior to the application being processed," Mr Bowden told reporters.
"We decided to send that to the courts so that they could take a thorough examination of all the issues and run through the process."
Kirsty Howey from the NT Environment Centre said she welcomed the charges, though more still needed to be done to stop illegal land clearing.
"Repeated instances of alleged unlawful clearing show we have a systemic problem in the Territory," she said.
"People across the Territory are rightly concerned about the risk that the cotton industry poses to the Territory's nature and rivers."
The charges mark the first prosecution filed for alleged unlawful land clearing in NT history.
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