Evidence could be destroyed and suspects alerted if journalists contested covert search warrants before they were carried out, the Australian Federal Police (AFP) has warned in a submission to a press freedom inquiry.

Key points: Media bosses are pressuring the Federal Government to strengthen press freedom

Media bosses are pressuring the Federal Government to strengthen press freedom The AFP is pushing back against that, arguing the proposal would undermine its effectiveness

The AFP is pushing back against that, arguing the proposal would undermine its effectiveness Federal Police say they need to be able to examine reporters to protect national security

Federal Parliament's intelligence and national security committee is investigating the impact of law enforcement powers on press freedom, after the AFP searched the home of a News Corp journalist and the ABC's Sydney headquarters in June, over separate stories based on leaked information.

Both media organisations want reporters and their employers to be able to contest applications for search warrants but the AFP rebuffed a terms of reference considering the change.

"Search warrants ... are often the first point at which the investigation becomes overt, or public," the submission states.

"However, it is often very important to the integrity of an investigation that persons of interest are not made aware of the investigation until such time as the warrant is executed.

"An opportunity to make representations or submissions at the time of issuance would undermine investigations by alerting suspects and providing opportunities to destroy evidence."

The AFP submission argued any form of contested hearing over covert powers would fundamentally undermine its effectiveness, and the ability of police to conduct an investigation.

The submission — which called press freedom a "fundamental pillar of democracy" — also said any restrictions on investigative powers over journalists could impact the AFP's ability to get the full facts of a case and of the Attorney-General to make an informed decision about prosecuting.

Legal challenges for AFP media raids

The ABC and News Corp are legally challenging the use of search warrants.

As part of its legal action, the ABC is asking the Federal Court of Australia to declare the warrant executed on June 5 invalid.

ABC managing director David Anderson said the broadcaster was also challenging the constitutional validity of the warrant "on the basis that it hinders our implied freedom of political communication".

Outgoing AFP Commissioner Andrew Colvin denied the June raids were designed to intimidate, but refused to rule out possible criminal charges being laid against three journalists.

"It's very rare and I think the public should draw quite a bit of comfort from the fact that these aren't every day," Mr Colvin said earlier this month.

"Two search warrants in those two days I don't think represents a grave attack on press freedom in this country."

The inquiry by the Parliamentary Joint Committee on Intelligence and Security is expected to hear from media, government agencies and other stakeholders before reporting back to Parliament in October.