The move has left thousands of passengers stranded around the country, forcing competitors to step in.
Bonza is the first carrier to launch in Australia in 16 years.
Dominated by two companies, aviation remains one of the nation's "most concentrated industries" according to Australia's consumer watchdog.
"We apologise to our customers who are impacted by this and we're working as quickly as possible to determine a way forward that ensures there is ongoing competition in the Australian aviation market," the airline said in a statement.
Mel Watkins, who was due to fly to Launceston for a family holiday told the Australian Broadcasting Corporation (ABC) that she was "absolutely shattered" by news her flight had been axed.
"I thought it's an Australian airline, and we'd be better off supporting a small company, but it turns out no."
Responding to the cancellations - which impacted departures across Queensland and Victoria - Australia's Transport Department set up an emergency help hotline for passengers on Tuesday.
Qantas Group and Virgin Australia - which account for 95% of the nation's domestic aviation market according to its airport authority - both also offered to step in and assist anyone stranded mid-journey.
Based in Queensland's Sunshine Coast, Bonza launched in 2021, promising low-cost fares and improved regional connectivity via a suite of new destinations.
After a long-delay while it awaited regulatory approval - it finally took to the skies in 2023 but aircraft shortages and low patronage saw it slash several routes in quick succession.
Those setbacks, combined with its inability to secure access to take-off and landing spots in the lucrative Sydney market quickly sparked speculation over its future.
Bonza's eight planes - a fleet of Boeing 737-Max - were repossessed by creditors on Tuesday according to local media, but the airline has not publicly addressed the claim.
Australia's main transport union is now seeking an urgent meeting with the airlines leadership to discuss how the sudden closure will impact workers.
"Bonza must ensure staff are prioritised and informed as this process plays out," the national secretary of the transport workers union, Michael Kaine said, according to the Guardian.
Mr Kaine also criticised the "unchecked corporate greed" in the aviation industry that's led to higher fares and warned that any carrier attempting to break into the market "has little chance of survival".
By Hannah Ritchie