The comments will spark outrage from Australia's major media companies,which have already condemned the raids on Smethurst's Canberra home on Tuesday and the ABC's Ultimo headquarters on Wednesday.

"I reject the claim over the last few days we're trying to intimidate journalists or conduct a campaign against the media,"Mr Gaughan said."The AFP is a strong supporter of press freedom. The media plays an important role in today's society in keeping the Australian community informed."

Smethurst on Thursday said she felt intimidated by the raid on her home,which involved police going through her underwear drawer in search of a USB drive.

Mr Gaughan claimed the AFP took"additional care to protect the confidentiality of other personal or professional information that was not subject to the warrant".

Asked how rifling through the underwear of a female reporter constituted extra care,the acting commissioner said that was"standard procedure"during the execution of search warrants.

"We were looking for USBs. By their nature,they're quite small and quite easy to conceal in different locations. That's why the search was conducted in accordance with our standard procedure in that we would always search those particular locations.

"We ensured,due to her privacy,when that search of that particular location in her house was undertaken,it was done by two female officers."

Mr Gaughan also raised the prospect of further raids on media organisations in the coming days or weeks. It is understood the AFP recently notified News Corp of plans to execute search warrants on the media group's Holt Street headquarters in Sydney.

"I'm not going to give a blow-by-blow description[of] where the investigation is at,and nor would you expect me to,"Mr Gaughan said.

"The investigation is complex and ongoing. Potentially,we may do more search warrants."

He said the warrants on Smethurst and the ABC were deliberately executed on consecutive days because that was when the AFP had the most resources available and denied the timing of the May 18 election factored into the AFP's decisions about when to apply for and execute search warrants.

"I made the decision of timing. That was my decision."

He stressed police never updated the government about the investigations but noted he"would be surprised if our investigators at some stage did not have some conversations"with the Defence Department,which referred the leaks to police.

Media raids:what we know

• Police say two people disclosed secret information to journalists
• The ABC published a series of stories called the Afghan Files in July 2017,which detailed secret Defence Force documents pointing to possible unlawful killings by Australian special forces soldiers
• News Corp's Annika Smethurst published a story in Sunday newspapers in April 2018 that pointed to correspondence between Defence secretary Greg Moriarty and Home Affairs secretary Mike Pezzullo,suggesting the Australian Signals Directorate should be able to"proactively disrupt and covertly remove"domestic cyber threats"by hacking into critical infrastructure"
• The AFP began the ABC investigation in July 2017 and the News Corp investigation in April 2018
• AFP officers had"some conversations"with the referring government agencies during the investigations
• Police say no ministers or ministers'offices were briefed during the investigations,until the search warrants were being executed
• AFP has been negotiating with the ABC about handing over material since the investigation started
• The AFP obtained warrants from an ACT magistrate and a NSW court registrar
• The warrants were deliberately executed on consecutive days because that was when the AFP had digital forensic experts available
• The AFP says it did not factor in the timing of the federal election
• Both investigations are ongoing
• One related court case is under way,involving former military lawyer David McBride,who has pleaded not guilty to charges in relation to disclosing documents to the ABC