The Defence Department has taken back a notebook containing information that could cause "substantial harm" to national security after it was handed to The Canberra Times in another major security breach.

Following questions from the newsroom on Thursday, Defence moved to lock down and then remove the notebook, which belongs to a top Defence official, on Friday afternoon.

A member of the public claims to have found the notebook earlier this month, along with three security passes and a personal letter addressed to the official.

Following an assessment of the notebook on Friday morning, the department told The Canberra Times that publishing its contents "could cause substantial harm to national security, in particular with respect to intelligence arrangements and related activities".

The department also requested The Canberra Times withhold the identity of the senior official involved in the breach, as "publication of such information may give rise to a foreign intelligence threat".

"An assessment by the department's senior officials of the hand written material it contains is that, in addition to personal information, it includes sensitive and classified national security information, in particular with respect to intelligence agencies," associate secretary of Defence Rebecca Skinner said.

How the items fell into the hands of the public remains unclear, but it is not believed they were stolen.

The senior official is understood to have written the notes while working with the Australian Signals Directorate in 2016. It is believed the notebook was later lost, along with the letter and security passes, one of which conferred top secret clearance.

Defence has since launched a full investigation into the breach.

Soon after a Defence officer secured the notebook on Friday, officials from Defence and the Department of the Prime Minister and Cabinet arrived at The Canberra Times to negotiate access to the document.

The notebook, along with the security passes and letter, were returned, but redacted copies were provided to the newsroom.

"Notwithstanding that the passes have no ongoing validity, in the wrong hands they may still be abused, and government policy and procedure requires that such passes be returned for destruction by the relevant government agency," Ms Skinner said.

Handwritten notebooks containing classified information are subject to the same security protocols as printed or digital documents, but the onus is on government officials to keep them safe.

On Thursday, head of the ANU National Security College Professor Rory Medcalf said handwritten notes about classified material "should be in themselves classified, and handled and stored as such".

"But it's obviously hard to enforce," Professor Medcalf said.

The Department of the Prime Minister and Cabinet launched an "urgent investigation" into another security breach on Wednesday after the ABC revealed it had obtained thousands of sensitive cabinet documents accidentally sold off at a second-hand furniture store in Fyshwick.

Dubbed "The Cabinet Files", the ABC said the documents span more than a decade, covering the Howard, Rudd, Gillard and Abbott governments, and should not have been made public for another 20 years.

On Thursday, ASIO took back the documents from the ABC, as part of negotiations between the broadcaster and the department.

Many of the files also contained national security information, the ABC reported.

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