The Indonesia-bound military plane was stopped in the northern city of Darwin for refueling when five galahs, also known as the rose-breasted cockatoo, and two parrots were discovered in bags on board, Macquarie Radio reported.
The Australian Customs and Border Protection Service said the pair were questioned on Thursday in Darwin.
“As a result of questioning no charges were laid. One Indonesian national was issued with a warning,” the service said in a statement.
Immigration Minister Scott Morrison said both had now left the country and offered little detail.
“The status of whether it’s a pilot, a crew member, or whatever, is, I think, not relevant to the case,” he said.
“We take these issues very seriously regardless of who is engaged with them and that’s what we did on this occasion,” Morrison said. “If there’s an offence that has been committed, then the necessary investigations and inquiries need to be undertaken.”
Morrison said the incident would not have an impact on relations between Australia and Indonesia, which have been strained in recent weeks by allegations that Canberra tapped the phone of Indonesian President Susilo Bambang Yudhoyono’s phone.
Prime Minister Tony Abbott said the matter was being investigated.