Three passengers from a Jetstar flight that disembarked in Sydney without proper health checks have been referred to police.

The trio are the last remaining passengers to be screened among the 137 aboard JQ520 that landed in Sydney from coronavirus-hit Melbourne on Tuesday night, just hours before the NSW-Victoria border closed.

All 137 were allowed to disembark in Sydney without COVID-19 health checks – a breach of NSW health orders.

NSW Health said 89 were called back for screening before they left the airport.

The remaining 48 passengers have since been contacted after the federal health department stepped into and worked through Wednesday night to help with urgent tracing. Arrangements have been made to screen 45.

The three outstanding passengers – including one who has refused to be screened – have been referred to NSW Police.

“There was an issue at the airport where passengers were disembarked when the health screening team were screening another airline,” NSW chief health officer Dr Kerry Chant said on Wednesday.

A NSW Health spokesperson later said airline staff hadn’t followed agreed protocols when they let passengers from flight JQ520 leave the gate area before health staff had finished screening an earlier flight.

But NSW Health said the passengers had been screened before leaving Victoria, including temperature and ID checks.

“As a result of this breach, flights will now not be allowed to land in NSW until NSW Health teams are in place to screen them,” the spokesperson said.

A Jetstar spokesman said on Wednesday the airline had assisted NSW Health in finding most passengers before they left the terminal.

The airline also provided health authorities with the aircraft manifest to help contact passengers.

On Thursday, federal Health Minister Greg Hunt said his department had intervened to help NSW authorities with contact tracing and tightening domestic flight protocols.

“We have to focus on making sure that everything that is being done at the state level is being done at the right level,” Mr Hunt told the Nine Network.

On Thursday, Jetstar Group chief executive Gareth Evans conceded the breach was “unfortunate”.

“They [the screening protocols] are different in every state and that causes confusion,” he told the ABC.

“These have been developed and changed very quickly over a number of days.”

All passengers who disembarked the flight should be in 14 days of self-isolation as part of NSW coronavirus protocols.

“If anyone’s travelled in breach of orders, we’ll refer them to police and take the appropriate action depending [on] if anyone is symptomatic,” Dr Chant said.

NSW Greens MP Cate Faehrmann called on state Health Minister Brad Hazzard to investigate the incident after he said earlier that all passengers arriving from Victoria would be screened at Sydney Airport.

“It’s gobsmacking that such an event could occur in NSW after the Ruby Princess debacle,” Ms Faehrmann said.

-with AAP