VIRGIN Blue has sent a $500,000 bill to the manager of air navigation services after more than 120 of its flights were delayed from landing or taking off at Sydney Airport for up to an hour on Friday.

Airservices Australia struggled to man the air traffic control tower again over the weekend, resulting in the delay of 80 Virgin flights on Sunday, forcing the airline to accommodate about 180 passengers at hotels in Melbourne after planes missed the curfew into Sydney.

Thousands of passengers were delayed after several air traffic controllers called in sick. Airservices had to slash aircraft movements at the airport from 48 an hour to 30.

Virgin said it had sent Airservices a bill for $500,000 yesterday because the delays due to a lack of air traffic controllers were getting worse.

"It's been going on all year and it's not getting better, it's getting worse," a spokeswoman said. "It is seriously inefficient and it affects us.

"It's not that unusual to have air traffic controllers underresourced at Sydney Airport."

Airservices has blamed the delays on an alleged campaign by controllers who it has accused of taking unwarranted sick leave and refusing to work overtime.

The air traffic controller's union, Civil Air, and Airservices have been locked in a stand-off for months over pay and conditions ahead of the expiry of a collective agreement in December. The only aspect both parties can agree on is the high likelihood of further delays at airports.

Airservices Australia withdrew an application to the Industrial Relations Commission on Saturday seeking a stop to what it dubbed "covert action" after the union agreed to post an alert to members that they were required to work "reasonable overtime".

Civil Air's president, Robert Mason, denied the suggestion that controllers were taking covert action, and said they were merely trying to get Airservices to reveal the full contents of the proposed wages deal.

"In the meantime, we are trying to hold together a system that has got more and more people leaving all the time," he said.