Sydney Airport has issued an unreserved apology after a security breach left thousands of passengers stranded and as budget airline Jetstar says it will seek damages over the disruption.

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A power failure caused a security screening checkpoint in the T2 terminal to malfunction on Tuesday afternoon, resulting in 16 passengers walking through without being screened.

Sydney Airport ordered the re-screening of the entire terminal, including many of those already on board planes awaiting take off.

The airport has bought advertising space in Sydney’s major newspapers for Thursday apologising to all passengers affected by the incident.

“Sydney Airport wishes to apologise to all passengers who were inconvenienced by Tuesday’s screening failure at T2,” the advert signed by Sydney Airport CEO Richard Balding says. “We want to learn all we can to make sure that there is no repeat of the disruption.”

Of the 29 flights cancelled because of the security lapse, 15 were Jetstar flights.

The airline on Wednesday said it would discuss damages with Sydney Airport over the disruption, which left 2000 of its passengers stranded overnight.

“We will be having discussions with Sydney Airport to seek damages for what happened,” a Jetstar spokeswoman told AAP.

“We will be looking for some form of compensation as there has been a huge disruption to our service.”

A Sydney Airport spokesman said the organisation would wait to hear from Jetstar before commenting.

All of Jetstar’s passengers were expected to get to their destinations on Wednesday.

A Qantas spokesman said a couple of its regional flights had been affected by the incident but all planes were running on time.

All other flights are expected to be running on scheduled on Wednesday and extra flights had been put on to clear stranded passengers.

An investigation into the incident is underway.