The company will cut around 80 jobs by the end of the week from its Pilbara sites and Perth office.
Around 30 roles will go from the Pilbara, with a further 50 Perth positions affected.
The company predicts the job cuts will save around $15 million, but will pay one-off restructuring costs of $3-3.5 million.
As a result, Atlas has increased its annualised cost savings target for the 2015 financial year to $75-100 million from $65-90 million.
The company has also lowered its all-in cash cost guidance for FY15 from $65-70 per wet metric tonne to $64-68/wmt and said it would target the lower end of the target.
Atlas said the reduced workforce would not impact its FY15 guidance of 12.4-13 million tonnes at C1 costs of $46-49/t and the company said it would continue to target the upper end of the production target.
"It's imperative Atlas maintains a competitive cost base in light of current market conditions," Atlas managing director Ken Brinsden said.
"We regret to see many good people leave our business.
"However these changes are necessary and will help ensure our longer term sustainability.
"Cost savings and strong productivity through our operations are delivering great results."
It comes after Atlas announced a reduction in its board on Tuesday from eight members to six.
All remaining directors have offered to reduce their remuneration by 15% as of Monday.
Baillieu Holst analyst Adrian Prendergast maintained his hold recommendation and 25c price target despite the cost cuts.
"We maintain the view that the current backdrop of iron ore price volatility and excessive uncertainty has removed the investment appeal of Atlas (and its iron ore peers) even at depressed share price levels," he said this morning.
The company's cost-cutting measures follow similar moves by fellow Pilbara producers BC Iron and Fortescue Metals Group last week.
However, Atlas has higher cash costs than its Pilbara peers and is considered most vulnerable to further drops.
Moody's Investors Service downgraded Atlas' outlook to negative on the expectation that the iron ore would remain weak into 2016.
"Given the further deterioration in the iron ore price, we see negative pressure building on Atlas' cashflow generating ability and a depletion in its previously solid liquidity position," Moody's analyst Saranga Ranasinghe said.
The agency noted Atlas' cash balance of $A204 million at September 30, but said the company was likely to be using its cash to fund operations.
Meanwhile, UBS on Friday upgraded Atlas from a sell to neutral.
Atlas said it had a good month in October, shipping 1.4Mt at all-in costs of $A67/wmt.
Shipments so far this quarter are 2.54Mt and the company said it continued to diversify its customer base, selling ore to customers in South Korea and the west coast of India for the first time.
Atlas shares dropped 1.9% to 15.7c, while the iron ore price rose $US2 overnight to $71.25/t.