A Queensland  couple are desperately seeking answers from Virgin Australia after the airline lost their pet cat Cookie in transit.

Jessica and Jack Thomas put their beloved "fur baby" on a flight from Brisbane to Cairns along with their dog Rambo, but only one of their pets arrived at the final destination.

In a desperate plea on Facebook, Jessica said only Cookie's cage and a blanket arrived at the airport, but their cat was nowhere to be seen.

"We are now being told that Cookie escaped from his cage (no word on how) on the tarmac while in Brisbane," Mrs Thomas wrote on Facebook.

"I am absolutely heartbroken and just want my fur baby home."

Mr and Mrs Thomas had booked Cookie and Rambo's transit ticket on-board Virgin flight VA785. They used animal transport company JetPets who in turn use Virgin Australia aircraft to transport their cargo.

"No one has given us any answers," Mrs Thomas said. "We have been told that Cookie left the warehouse in a crate. Virgin have told us they are doing everything they can.

News.com.au understands Cookie escaped from his crate prior to boarding the aircraft, possibly because the cage door of the enclosure wasn't secured properly and not all of the required additional cable ties were in place.

While the investigation into Cookie's disappearance is still ongoing, it is understood the airline has conducted three searches for Cookie including resourcing additional operational team members to search the area around the airport where Cookie was last seen.

"Virgin Australia is saddened by the disappearance of Cookie," a spokesperson said in a statement to news.com.au.

"This is a distressing situation for his owners and we are providing regular updates to them.

"We are truly sorry for this incident and we are doing all we can to locate him.

"We take pride in transporting our guests' pets and our teams follow stringent guidelines to ensure the highest of safety standards are upheld. We will continue to investigate how this incident occurred and review and update our processes accordingly."

Speaking to Nine, Mrs Thomas said they were very anxious about putting their pet on a plane, and now their apprehensions are warranted.

"We were very nervous and now we realise we had reason to be," Mrs Thomas said.

"I just want my cat back."