In a video message released on Friday, Vanessa Hudson acknowledged Qantas had work to do in winning back trust among travellers.
"I know that we have let you down in many ways," she said.
"We haven't delivered the way we should have and we've often been hard to deal with.
"We understand why you're frustrated, and why some of you have lost trust in us."
The airline was determined to fix the issues, improve the experience of flyers and better support its workers, she said.
"We want to get back to the national carrier that Australians can be proud of," said the airline chief, who took over from Alan Joyce who left on September 5.
"We understand we need to earn your trust back, not with what we say, but what we do and how we behave."
The apology came as a Senate committee heard fresh concerns that Qantas had been throwing its weight around.
Speaking under parliamentary privilege, Canberra Airport chief executive Stephen Byron told the inquiry sitting in Perth that Australian airports had copped "unlawful behaviour" from Qantas, with the airline acting as if it were "above the law".
"Things need to change with Qantas ... our opinion is that Qantas will not change unless they're brought to heel by a regulator, or by the highest court in the land," he told the committee examining bilateral air services agreements.
Mr Byron said reforming the slot system - which authorises take-offs and landings at airports - would be "most critical" to achieving competition, including the need to enforce a "use it or lose it" rule.
He said for domestic flights, if an airline had high cancellation rates the slots should automatically be taken away.
Committee chair and Nationals senator Bridget McKenzie said while the apology from Ms Hudson was welcome, it came on a day when it was revealed Qantas cancelled 849 flights in August, an eight per cent increase on July cancellations.
"By cancelling 849 flights in August, thousands of Qantas customers have been forced to seek alternative travel arrangements," she said after the hearing concluded.
The senator said there were decisions the government could make today, including making more take-off and landing slots available at Sydney Airport.
Meanwhile, farming groups have voiced concerns about the damage to the trade relationship with Gulf nations from the Labor government's recent decision to knock back a doubling of flights requested by Qatar Airways.
Pastoralists and Graziers Association WA president Tony Seabrook told the inquiry the industry was "hurting".
"There are a lot of producers that have had enough ... this is the final straw," he said.
Throttling airline capacity prevents the sector from expanding even as the failure to return flights to pre-COVID levels has already hurt exports.
"Any move to restrict flights to Doha should be carefully scrutinised," WAFarmers chief executive Trevor Whittington said.
Senator McKenzie has criticised Transport Minister Catherine King's decision to block Qatar Airways' bid to double the 28 weekly services it offers in Australia, after it was revealed Qantas had lobbied against the increase.
Ms King has claimed the decision was made in the national interest but hasn't provided the reasons behind it.
But the opposition has accused the government of running a "protection racket" for Qantas.
The airline's reputation has taken a hit after a string of issues, including a High Court defeat which found the carrier illegally sacked almost 1700 workers during the COVID-19 pandemic.
The committee will hold another two public hearings in Brisbane and Canberra, before it reports back by October 9.
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