The Department of Prime Minister and Cabinet has confessed it is the one that lost the documents at the centre of the ABC's reporting on The Cabinet Files.

Australia's domestic spy agency has taken possession of hundreds of cabinet documents obtained by the ABC, following one of the biggest security breaches in Australian history.

The ABC and the Prime Minister's Department reached an agreement on the return of the documents, which protects the ABC's source.

In a statement, secretary Martin Parkinson said the breach casts his department in poor light and has implications for the rest of the Australian Public Service.

"The AFP investigation into how and when the classified documents, obtained by the ABC, left the Commonwealth government is ongoing," Mr Parkinson said.

"It is now reasonably evident that the cabinets and documents, which are the subject of the AFP investigation, came from the Department of the Prime Minister and Cabinet.

"While it remains unclear, it is likely this occurred some time ago."

Department working closely with AFP on investigation

Mr Parkinson said he would launch a review of the department's security procedures, practices and culture.

"We continue to work closely with the AFP to support its investigation," he said.

The Cabinet Files is one of the biggest breaches of cabinet security in Australian history.

Thousands of pages of documents, some marked "top secret" and "AUSTEO" (for Australian eyes only), were contained in the sold-off filing cabinets.

Some of the revelations from the documents include:

Officers from ASIO, the domestic intelligence agency, retrieved papers in Canberra, Melbourne and Brisbane late on Thursday evening, where they had temporarily been stored in safes on ABC premises.

The ABC had released a statement in parallel with the Department of Prime Minister and Cabinet about the return of the documents.

"The ABC and the Department of Prime Minister and Cabinet have agreed on the securing of and the return of the documents which were the subject of the ABC's Cabinet Files reporting to the Commonwealth," the ABC said.

"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."