Federal ministers have been warned by the Government's own information watchdog that messages sent on mobile phone applications, such as WhatsApp, should be released publicly, if requested.

A number of Cabinet ministers have confirmed they use such apps to communicate with one another.

These include WhatsApp (owned by Facebook), Slack and Wickr — all smartphone applications that send messages over the internet.

Labor said it was concerned frontbenchers were using the services to escape obligations under the Freedom of Information Act (FOI), which allows the public access to documents held by ministers and departments.

But the agency overseeing the FOI Act, the Office of the Australian Information Commissioner, cautioned ministers they could not hide from scrutiny using the apps.

"The FOI Act applies to an 'official document of a minister' regardless of the way it is stored," Australian Information Commissioner, Timothy Pilgrim, told the ABC.

"For example through an app, or whether it has been transmitted via a government or non-government server," he said.

"Every person has a legally enforceable right to obtain access to an 'official document of a minister', other than an exempt document.

"Official documents are those documents held by the minister, in their capacity as a minister, that relate to the affairs of an agency or department."

A spokesman for Attorney-General George Brandis agreed the messages needed to be handed over, if requested.

"All communications or records of a minister which relate to his or her duties are potentially subject to FOI," he said.

Shadow Attorney-General Mark Dreyfus said departments must heed the advice and search messaging applications when undertaking FOI requests.

"Use of all of these digital technologies is just as subject to the Freedom of Information Act as a written document," he said.

"The information commissioner has made it crystal clear."

Security risks of using apps yet to be assessed: official

A high-level official from the Prime Minister's department told a parliamentary committee last year searches could not be conducted on platforms such as Wickr and Slack.

It is unclear whether any messages sent on the apps have been released under the FOI Act.

Fairfax Media also reported WhatsApp could pose a security risk, saying it had not been approved by the intelligence agency the Australian Signals Directorate.

The official told the committee the potential security risks of using such applications had not been assessed.

"I call on the Government to give a reassurance that they will stop using the WhatsApp messaging system, which is not secure," Mr Dreyfus said.

The Attorney-General's office said rules were in place for classified communications.

"All classified communications happen appropriately on secure channels," it said.

"There is a protocol around the security of mobile devices."

Trade Minister Steve Ciobo described concerns about WhatsApp as a "storm in a teacup".