An investigation has been launched as to why a Qantas jet was cleared to cross Sydney Airport’s main runway while another aircraft was landing, amid reports of staffing woes in the air traffic control tower.

The Australian Transport Safety Bureau announced it is investigating a “breakdown of coordination” between QantasLink Bombadier DHC-8 from Canberra and another Qantas flight on a Boeing 737 from Queenstown.

It is believed air traffic control cleared the Boeing 737 — flight number QFA124 — to cross a runway moments after the QantasLink flight had touched down on the same runway.

“Air traffic control. . . cleared the 737 on runway 25 to cross runway 34L while the DHC-8 was in the landing roll on runway 34L,” a statement from the ATSB said.

“ATC detected the conflict and advised both crews, with the 737 stopping after the holding point.

“The investigation is continuing.”

The incident comes as AirServices Australia faces criticism over staffing levels in the Sydney Tower, after a number of incidents caused ground delays on up to four occasions.

An Airservices Australia spokesperson says the company is assisting with the ATSB, but did not comment further due to the matter still being under investigation.

“Safety is Airservices’ top priority,” the spokesperson said.

A Qantas spokesperson confirmed both aircraft were cleared to proceed following instructions from air traffic control.

“We will support the ATSB in the investigation,” the spokesperson told The Nightly.

Airlines for Australia CEO Stephen Beckett says the delays are “ongoing and persistent” thanks to staffing issues at the Sydney tower, which is delaying flights around the country.

“We are constantly seeing an inability to staff the air traffic control towers around the country and that is leading to considerable disruptions to our airlines and passengers,” Mr Beckett reportedly told the Pacific Airline Leader Summit last week.

“It’s not just the one-off.”