Domestic services were disrupted between 10am and 1pm, when departures were forced into four-minute intervals, throttling the normal flow of traffic through Sydney Airport.
Qantas and Jetstar reported delays of around an hour during the slowdown, while Virgin Australia services were held up by about 40 minutes.
Airservices and the Civil Air union both rejected suggestions the absences were linked to the World Cup semi-final between England and Argentina, which took place on Thursday morning.
The disruption is the third staffing-related incident in a month to hit Sydney’s air traffic control operations and ripple through airline schedules.
On July 5, the absence of two controllers triggered a reduction in both arrivals and departures, coinciding with the start of the NSW school holidays.
A similar staffing shortfall in late June also forced throughput to be cut and flights to be delayed.
