The trial of OM (Manganese) Ltd, a subsidiary of OM Holdings Ltd, began in the Darwin Magistrates Court on Monday.
It is alleged the miner damaged and desecrated the Two Women Sitting Down sacred site at the Bootu Creek manganese mine, about 170km north of Tennant Creek.
The company has already said it will plead guilty to a charge of damaging the site, but will fight two other charges related to desecrating the site.
Andrew Collett, acting for the Aboriginal Areas Protection Authority told the court that on March 19, 2011, a blast was set off by the miner about 40 metres away from the sacred site.
The next day the rock formation that had been there since time immemorial had collapsed, Mr Collett said.
“An ordinary mining company in similar circumstances would not have proceeded with mining in the way the defendant did,” Mr Collett said.
He said the site had great significance to the Kunapa people and related to a dreaming story about a marsupial rat and a bandicoot that had a fight over bush tucker.
As the mythical creatures fought their blood spilled out, turning the rock a dark red colour that is now associated with manganese, he said.
He said the disappearance of the rock formation meant the site changed its shape significantly and it was harder to recognise the dreaming associated with it.