This week will see some of the busiest travel days of the year, with many people travelling with young children and lots of bags.
Virgin Australia told news.com.au staff are working hard to have guests on their way as quickly as possible.
"Today is one of the busiest days of the year for travellers returning from holidays which has resulted in delays at our check-in counters at Sydney Airport this morning," the airline said in a statement.
"Each of our check-in counters are fully staffed and we are working hard to have guests on their way as quickly as possible. During peak travel periods we encourage guests to check-in online, arrive at the airport early, and listen out for announcements made in the terminal."
Jetstar and Tiger, which share the terminal, appear to be unaffected.