Mining firm OM Manganese was found guilty on Friday - the first time a company has been successfully prosecuted in Australia for desecration of a sacred site.
The site is known as Two Women Sitting Down and is at Bootu Creek, north of Tennant Creek.
OM Manganese was fined A$150,000 ($134,000; Â£88,000).
Peter Toth, CEO of OM Holdings, which owns OM Manganese, said: "The company never intended to harm, damage or disrespect the sacred site."
"We sincerely regret the damage and the hurt caused and I unreservedly apologise to the site's custodians and traditional owners," he said.
Two Women Sitting Down is associated with Australia's Kunapa people.
OM Manganese was accused of causing the collapse of part of the site, including a distinctive rocky outcrop known as the Horse's Head, in July 2011.
Prosecutors told the Darwin Magistrates Court that the company performed explosive blasting close to the site to break up ground, Australian broadcaster ABC reported.
The company was permitted to mine in the area, but was advised to steer clear of sacred sites, and was warned in early 2011 that cracks were appearing in rocks at the Bootu Creek site, the broadcaster said.
Dr Ben Scambary, chief executive officer of the Aboriginal Areas Protection Authority, said that the site was of great significance to Australia's indigenous people.
"This site... relates to a dreaming story about a marsupial rat and a bandicoot who had a fight over bush tucker [native Australian bush food]," he said.
"As the creation ancestors fought, their blood spilled out, turning the rock a dark-red colour that is now associated with manganese."
Kunapa community representative Gina Smith said: "It will always remain a sacred site to us, but it has been ruined and we don't know what to do because this has never happened to the old people.
"It has been there for thousands of years as part of our culture and our story."
Indigenous Australians believe the land is the mother of creation, and is a living, breathing mass full of secrets and wisdom, the BBC's Phil Mercer in Sydney reports.
A mining company has been convicted of desecrating an Aboriginal site in Australia's Northern Territory.