The ABC said the Australian Security and Intelligence Organisation took the files after talks with the spy agency in recent days, though as part of negotiations the national broadcaster said it will still have access to the files.
The ABC had based its report on Cabinet documents found within a filing cabinet purchased at a second-hand furniture store, which the AFP labelled as incomplete and outdated.
"You shouldn't be able to find information out because someone didn't check a set of filing cabinets, then they sold it at a second hand government furniture sale".
The ABC has refused to reveal who bought the cabinets and found the trove of documents, insisting they would "protect their privacy at all costs".
Australian Cabinet documents are usually kept classified for 20 years, before being made public in redacted form. According to ABC, an overwhelming majority of the cabinet files were classified, some as "top secret" or "AUSTEO", meaning they are to be seen by Australian eyes only.
"This has been achieved without compromising the ABC's priority of protecting the integrity of its source and its reporting, while acknowledging the Commonwealth's national security interests", the joint statement said.
"First, the cabinet document referred to by the ABC was given to and considered by the royal commission into the home insulation program by the Abbott government in 2014".
Trump's CDC Director Resigns After Getting Caught Buying Shares in Tobacco Company
The purchases totaled tens of thousands of dollars and included investment in one of the largest tobacco companies in the world. Fitzgerald became director of the CDC in July, bought stock in Japan Tobacco in August 2017, and sold it at the end of October.
Former Prime Minister Kevin Rudd says he has begun legal proceedings against the ABC in the wake of the national broadcaster publishing a story on the Labor government's fatal home insulation from leaked Cabinet documents.
The files released by the ABC also show that in 2007 the prime minister at the time, John Howard's national security committee gave serious consideration to removing an individual's unfettered right to remain silent when questioned by police.
ABC has not identified the buyer of the cabinets, who removed the locks with a drill and found classified papers spanning nearly a decade and four prime ministers, the most recent being Tony Abbott.
John Howard's National Security Committee (NSC) nearly removed the right to remain silent.
The papers left in the office - but not included with the sold filing cabinets - included Middle East defence plans, national security briefs, Afghan war updates, intelligence on Australia's neighbours and details of counterterrorism operations. On Wednesday, the Department of the Prime Minister and Cabinet (PMC) announced an urgent investigation. Those documents were eventually found by security staff, who saw them destroyed.