The Defence department expects Newcastle Airport's "uneven" runway to be fixed by Monday after a weekend of flight disruptions.
A department spokesperson said on Sunday that works on extending the runway had left a "depression" in the asphalt.
Some commercial pilots refused to use the runway on Friday and Saturday after several reported issues while landing.
Cancelled flights caused travel chaos for some airline customers, including missed concerts, stranded school groups and passengers struggling to find accommodation at short notice in Brisbane, Melbourne and Newcastle.
The airport is facing one of its busiest weeks of the year as the Supercars circus arrives in the Hunter for the Newcastle 500.
The Defence spokesperson said on Sunday that the Williamtown runway was operating at "reduced capacity due to the discovery of a section of uneven asphalt linked to major runway works".
Passengers took to social media to vent their frustration about cancelled flights and a perceived lack of communication.
Newcastle company AusSteel said in a Facebook post on Friday night: "You guys are an absolute joke understand you could have informed people hours ago instead you have them book alternate flights to cancel them again 3 hours later.
"I have had staff stuck in Brisbane since 11:00am and now they will have to fly to Sydney and get home at 1:30am would have been quicker to drive."
One passenger from Shepparton in Victoria wrote about "waiting on the streets of Sydney" after being forced to catch a train at midnight on Friday from Newcastle and finally securing a flight to Melbourne at 7am.
"No sleep for 32 hours, so cancelled my shift at work on Saturday as way too tired. Thanks for the Trip!" she said.
Newcastle Airport's online log of arrivals and departures shows several QantasLink and Virgin flights to and from Melbourne and Brisbane were cancelled on Saturday.
One passenger said on Facebook that she had missed seeing Ed Sheeran at Melbourne Cricket Ground.
Newcastle Airport said on Sunday morning that no flights scheduled for that day had been cancelled so far due to the runway issue.
Defence said the issue had been identified on Friday after a section of the newly laid runway had reopened to air traffic.
"Specialist crews and plant were mobilised, but overnight efforts to smooth out the depression were not fully successful," the spokesperson said.
"The situation is expected to result in some large commercial jet aircraft not being used to service Newcastle."
More personnel and equipment would be "mobilised" to "remedy the depression and restore normal traffic flows as soon as possible".
"It is expected normal operations will resume by 6am on Monday," Defence said.
One woman wrote on Facebook that students and teachers from her daughter's school had been stuck waiting at Melbourne Airport for four hours on Friday before being told at 6.15pm their flight had been cancelled.
"Trying to find accommodation for the night for 30 plus students and staff at such short notice is disgraceful," she said.
"They have now told them they will be split up as a group and put on whatever flights they can into Sydney tomorrow ... and then get their own way home from there!"
Some passengers expressed gratitude that airlines had prioritised safety.
