Early on Wednesday traffic around the domestic airport was backed up for a kilometre, while queues outside the terminal snaked back for up to 100 metres.
Sydney Airport CEO Geoff Culbert has acknowledged passengers will be trapped in long queues as they wait to board flights.
"I want to start by apologising to them for any inconvenience that they've experienced," he told Sydney radio 2GB on Wednesday.
"It's another busy day," he said.
The delays to processing passengers were primarily due to staff shortages.
"Everyone in the aviation industry has been rebuilding their business from the ground up," Mr Culbert said, adding it was impossible to recruit enough staff and the airport's security provider had 100 vacancies.
"But then you add on that the COVID issues - on any given day up to 20 per cent of staff can't come to work due to COVID," he said.
At peak times like Easter holidays the airport would usually boost its resources, "but if you dont' have the staff then you can't do that", he said.
"We're doing the best we can - we're mobilising staff from all different areas of the airport ... but the bottom line is when you're operating at 60 per cent of staff capacity and you're back at almost 100 per cent of passenger numbers - then there's going to be a shortfall."
Easter Thursday is traditionally one of the busiest days for the airport with about 80,000 passengers expected.
"It's going to be really busy," he said.
Passengers are advised to arrive at least two hours before a domestic flight and three hours before an international flight.
"Be prepared, check-in online if you can and ... if you don't need to check-in a bag then try and avoid that - that's a major choke point in the system," Mr Culbert said.
"And be patient."