The federal government and Qantas have found a solution to the doggone dilemma that left the furry friends abroad after their owners had returned home.

Cats and dogs will be sent via Sydney to the quarantine centre in Melbourne when there is no option for them to be sent on a flight into Victoria.

Federal Agriculture Minister David Littleproud said the temporary arrangement was great news for Australians with pets stranded overseas due to the pandemic.

He said some pet owners had made the difficult call to leave their animals behind due to coronavirus travel restrictions.

"That is why we have worked with Qantas to offer an alternative arrangement for cats and dogs to be reunited with their families during these difficult times," he told AAP on Friday.

All pets returning to Australia must undergo quarantine at the Melbourne facility.

Almost 2800 dogs and cats have arrived in the country this year, including more than 1200 since May when air transport for pets restarted after a two-month pause.

That's about 60 per cent of the numbers from the same period last year.

Mr Littleproud said Qantas had proven it could meet Australia's strict biosecurity laws.

"Biosecurity will never be traded off and import conditions must be met in full before any pet can come to Australia," he said.

"I look forward to seeing Australians being reunited with their beloved pets and hope that this brings some happiness during a difficult period."

Pet movements remain restricted due to limited flights but the new deal will allow more back into the country.

The details of the arrangements will be available later this month.

Australian Associated Press