An experienced air traffic controller cleared a Virgin Australia flight for take-off during a near-miss incident at Australia’s busiest airport, Airservices Australia has revealed.

The safety incident — the third of its kind in just two weeks — unfolded about 10am on Sunday, when flight VA555 was cleared for take-off while Qantas flight QF728 had already been given permission to cross the runway.

The Australian Transport Safety Bureau (ATSB) said the Virgin crew had already applied thrust for take-off when they saw the Qantas 737 begin crossing the runway ahead of them from taxiway Lima.

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The Virgin pilots reduced thrust and brought the aircraft to a stop on the runway, the ATSB said.

Providing an update on the incident on Friday, Airservices Australia CEO Rob Sharp said the Virgin plane remained stationary after the controller immediately cancelled the clearance.

“The controllers immediately rescinded the clearance — they recognised that there was a Qantas aircraft 1.3km away approaching the runway,” Sharp said.

Airservices Australia CEO Rob Sharp. Credit: 7NEWS

Sharp disputed the ATSB’s characterisation that training was taking place in the tower at the time, saying the controllers involved were experienced and qualified and undergoing a routine endorsement process.

“A qualified, experienced controller advised clearance but immediately cancelled that clearance,” he said.

“There was a qualified controller who was also supervising.”

Sharp acknowledged it was standard practice for training and assessment to take place while passenger flights were operating, calling it “an industry-wide practice”.

He said Airservices did not initially report the incident because it did not believe it met the threshold for mandatory reporting.

Sharp said the decision was based on the clearance being immediately rescinded, the Virgin aircraft being stationary and the 1.3km distance between the aircraft being “quite substantial”.

However, he said Airservices would work closely with the ATSB as it investigated the incident.

“We’re quite open to reviewing the data that surrounds it,” he said.

“If there’s improvements to be made, we will make them.”

Sharp said he took “full accountability” for safety at Airservices and acknowledged ongoing staffing and rostering challenges in Sydney.

He said the organisation did not yet have a sufficiently “robust” system in place and needed additional air traffic controllers, with lengthy lead times to recruit and train them.

“We have a very highly professional, highly trained workforce in Sydney Tower and we’ve also got a lot of managers and support on the ground,” he said.

“So, we’re looking to minimise the impacts as much as we can while we’re working with all our stakeholders to improve the performance that we have.”

Sharp said Airservices had safety management systems in place, including a board subcommittee specifically focused on safety.

“I can assure the public that we absolutely look at all of these incidents for any learnings and continue to improve,” he said.

The incident follows two other recent near-misses at Sydney Airport, both of which are being investigated by the ATSB.

A QantasLink flight from Canberra and a Qantas 737 service from Queenstown came close to disaster on July 27, while a Jetstar pilot was forced to brake suddenly to avoid colliding with a Qatar Airways aircraft being towed across the tarmac on Sunday.

The incidents come as the ACCC seeks feedback on price rises proposed by Airservices Australia.

The organisation has proposed increasing the prices it charges airlines for enroute navigation, terminal navigation and aviation rescue and firefighting (ARFF) services.

Under the proposal, prices would rise by an average of about 15 per cent each year for five years from 2026-2027, leaving the weighted-average price 103.2 per cent higher by 2030-2031.

Airservices said the increases were needed to recover the costs of providing its services and fund future investment, while the ACCC is seeking submissions from airlines, the aviation industry and other interested parties before assessing the proposal.