The Transport Workers Union (TWU) said the incident, caused by a man who walked through exit doors into a secure zone at Melbourne Airport today, was "a long time coming".
The man was lost by security on CCTV after entering the area reserved for already screened passengers, the TWU said.
The union said in light of the incident it wanted a complete upgrade of all security across Qantas operations.
It is not thought the man had suspicious intentions when he entered through the wrong door, although the incident, which occurred at 9.30am (AEST), had been referred to the Australian Federal Police.
A Qantas internal investigation also was planned.
TWU national secretary Tony Sheldon linked events to a recent change in Qantas security contractors at the airport, from Chubb to MMS.
"When that happens, you see trained staff walk out the door and new staff come in with a whole new environment to deal with," Mr Sheldon said.
Qantas should improve security at all terminals and stop outsourcing work to contractors who were "untrained and unscreened", the TWU said.
Mr Sheldon said in 2009 staff held meetings after a man was killed at a Qantas terminal in Sydney during a bikie brawl.
"Here we are, two years and two weeks later and we have another nightmare in the terminal," Mr Sheldon said. "When is management going to get off their backsides and fix this situation?"
A Qantas spokesman said for unknown reasons, a man at the domestic terminal entered the secure area through the exit doors in the arrival hall.
"As a result we have to rescreen everybody that has already passed security into the secure zone," he said.
Five flights were expected to face delays of up to an hour, because hundreds of people would have to be rescreened, the spokesman said.
A disgruntled passenger told Sky News he thought Qantas had handled the situation badly.
Nobody from the airline told him the procedures for rescreening, he said.
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