The Australian Federal Police is bracing for fresh scrutiny over its decision to raid major media organisations after officers quietly abandoned a separate investigation into who leaked classified national security advice at the height of a major political dispute over border protection.

The leak, which Australia's top spy decried as "seriously damaging" and Labor claimed was orchestrated by the Morrison government to discredit proposed laws to fast track asylum seeker medical transfers, was referred to police by Department of Home Affairs secretary Michael Pezzullo earlier this year.

The Sydney Morning Herald and The Age can reveal federal police officers evaluated the referral but opted against launching a full investigation "due to the limited prospects of identifying a suspect".

The AFP's decision stands in contrast to its response to two other cases where confidential information was published, which culminated in raids this week on the home of a senior journalist in Canberra and the ABC's Sydney headquarters.