Ms Fyles, 45, held a snap press conference on Tuesday where she confirmed her intention to step down as chief minister and health minister.
She said she had made an oversight and did not declare a share parcel which came about after a BHP demerger.
Ms Fyles landed in hot water for holding Woodside shares before the latest share scandal. (Neve Brissenden/AAP PHOTOS)
"It was an error on my behalf and I don't have any excuse for that,'' she said.
"It was not deliberate, it was not intentional but it's unacceptable. For this reason I feel the honourable action is to resign as chief minister.
"I can assure Territorians that no decision I've ever made has been influenced by that small shareholding but high standards are expected from people holding high office."
The former schoolteacher took over from outgoing Labor leader and chief minister Michael Gunner, who resigned in 2022 after shepherding the NT through the COVID-19 pandemic.
Her resignation comes less than 24 hours after it was revealed she holds undisclosed shares in South 32, which owns the GEMCO manganese mine in the remote community of Groote Eylandt.
Earlier this year, Ms Fyles said the government would not investigate air pollution levels or health impacts after residents raised concerns over manganese dust in the community.
Deputy Chief Minister Nicole Manison is a likely contender to replace Natasha Fyles. (Amanda Parkinson/AAP PHOTOS)
She has faced growing pressure in the past few months of her tenure, with the GEMCO revelations the latest in a string of shares scandals.
She was forced to divest shares in Woodside, after media and federal politicians called into question potential conflicts of interest, in particular the government's large-scale expansion of the NT gas industry.
Both shares scandals were broken by the NT Independent, a small online news source that had been controversially barred from government press conferences.
Ms Fyles was referred to the NT's Independent Commissioner Against Corruption by an independent backbencher over potential conflicts of interest.
The party is deliberating over Ms Fyles' replacement, tipped to be Deputy Chief Minister Nicole Manison or Infrastructure Minister Joel Bowden.
Ms Fyles will contest her seat of Nightcliff at the 2024 election.
Infrastructure Minister Joel Bowden is considered a candidate for the NT's top job. (Neve Brissenden/AAP PHOTOS)
"It's been an absolute honor to serve as chief minister of the Northern Territory," she said.
"For now, it's farewell and I'll see you in 2024."
Ms Fyles took no questions after reading from her short statement.
Federal Member for Solomon in the NT, Luke Gosling, provided a brief statement that included no thanks for the outgoing chief minister.
"The resignation of the chief minister was the only acceptable course of action," he said.
"The NT government has a huge task ahead of it, they must learn the lessons of previous NT governments and work together, not focusing on themselves but rather on the Territorians they have been elected to serve."
The NT election will be held in August 2024.
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