The Australian Federal Police raided the ABC's offices in relation to a story on war crimes in Afghanistan on Wednesday, just one day after they raided News Corp journalist Annika Smethurst's home over a story about a government plan to spy on ordinary Australians.
Mr Morrison, who initially said he was "never troubled" by the law being upheld, has now distanced the government from the police operation which has sparked allegations of press intimidation.
"First of all let me say that my government is absolutely committed to freedom of the press, secondly these are matters that were being pursued by the AFP operationally at complete arm's length from the government, not in the knowledge of the government, not at the instigation of government ministers," he said after D-Day commemorations in the UK on Wednesday.
Mr Morrison said he understood the raids have caused anxiety from the press and more broadly, and had spoken with media organisation editors and briefed the opposition about the situation.
"I can understand, particularly for the journalists involved, this would have been very upsetting and a very anxious and concerning event. Of course, it would be," he said.
But Mr Dreyfus said the government would have sought to investigate the leaks behind the media reports.
"What we can't have is these hollow, hollow words from Mr Morrison saying that he believes in press freedom when these raids are happening right now in Australia," he told ABC's Radio National on Thursday.
"It's the government which referred these matters in the first place. It's the government which made a decision that these leaks - not all the other leaks that occur within government administration - warranted investigation."
Mr Morrison said that the investigation had been triggered by referrals from departmental heads before August 2018, when he became prime minister.
Mr Morrison said there were checks and balances around police investigations and no one in his government had any prior knowledge of the raids.
"It was not referred by government ministers or at their direction, it was referred by departmental secretaries," he said.
"And that is the process that departmental secretaries follow where they believe that there have been potential breaches and that's why the AFP is the agency that then investigates those and they are the ones who decide how they carry matters forward
"And for government ministers to be placed in the middle of that I think would be very troubling and that is what has not occurred here."
Home Affairs Minister Peter Dutton said he had no involvement in the AFP investigations and his office was only informed after the two warrants were executed.
The AFP insisted there was "no link" between the ABC and Smethurst raids and confirmed Mr Dutton "was not notified prior to the execution of the warrants".
"Both, however, relate to separate allegations of publishing classified material contrary to provisions of the Crimes Act which is an extremely serious matter that has the potential to undermine Australia's national security," an AFP spokesperson said.
The ABC vowed to protect its sources as officers searched through staff emails and phones.
"It is highly unusual for the national broadcaster to be raided in this way," ABC managing director David Anderson said in a statement on Wednesday afternoon.
"This is a serious development and raises legitimate concerns over freedom of the press and proper public scrutiny of national security and defence matters."
Mr Anderson said the ABC stood by its journalists, would protect its sources and continue to report "without fear or favour" on national security and intelligence issues.
The media union said the dual raids were a disturbing attempt to intimidate legitimate journalism in the public interest.
"This is nothing short of an attack on the public's right to know," MEAA media section president Marcus Strom said in a statement.
"Police raiding journalists is becoming normalised and it has to stop."
The union argued national security laws passed in recent years had been designed not just to combat terrorism but also to persecute whistleblowers who sought to expose wrongdoing.
Strom demanded to know who'd ordered the raids and why they only came after the federal election, given the stories were published in 2017 and 2018.
The ABC said Wednesday's raid was in relation to a July 2017 story that revealed hundreds of pages of secret Defence Force documents that gave "an unprecedented insight into the clandestine operations of Australia's elite special forces in Afghanistan including incidents of troops killing unarmed men and children".
The ABC reported at the time that some of the cases detailed in the leaked documents were being investigated "as possible unlawful killings".
The Australian Federal Police said Wednesday's raid was "in relation to allegations of publishing classified material" and followed a referral on July 11, 2017, from the Defence Force chief and the then-acting secretary for Defence.
The AFP said the ABC warrant was not linked to the Canberra raid 24 hours earlier.
The Australian Lawyers Alliance says the raids are a disturbing attempt to harass and bully journalists and their sources.
"This is frightening stuff," spokesman Greg Barns said in a statement.
"Both stories are clearly within the public interest. This intimidating behaviour by the police poses a serious risk to our democracy."
Labor demands explanation
The police action targeting reporters has alarmed many journalists, who have raised concerns about freedom of the press.
Labor has requested a briefing on the raids from the Home Affairs Minister Peter Dutton's office.
"Minister Dutton must explain what he knew about these two raids – one on a journalist’s home and one on the ABC," Labor home affairs spokesperson Krisina Keneally said in a statement.
"Freedom of the press is an essential component of our democracy."
Speaking before the ABC raid, Attorney-General Christian Porter said it was likely Mr Dutton was given a "heads up" about the search on Ms Smethurst's property.
"It's usually the case that in matters that are sensitive - and clearly this is - that there'll be a quick briefing to alert someone that it's going to happen when they’re the responsible minister."
However, he rejected any suggestions of government involvement in the decision or the timing of the raid.
Centre Alliance Senator Rex Patrick believes the intimidation of a journalist is a "worrying development".
He plans to follow up the matter in Senate estimates hearings later in the year.
"There are serious questions about the timing of the raid, why the raid occurred only at her home, and indeed what steps had been taken prior to the raid being conducted," he told ABC Radio on Wednesday.
News Corp labelled the raid "outrageous and heavy-handed".
"This raid demonstrates a dangerous act of intimidation towards those committed to telling uncomfortable truths," a spokesperson said.
The ABC and federal police officers have agreed to a two-week hiatus in which a search warrant served to the ABC can be challenged.
The BBC issued a statement on Wednesday evening, labelling the raid an "attack on press freedom which we at the BBC find deeply troubling".
"At a time when the media is becoming less free across the world, it is highly worrying if a public broadcaster is being targeted for doing its job of reporting in the public interest."
ABC head of investigative journalism John Lyons on Wednesday said he'd "never seen an assault on the media as savage as this one we're seeing today".
The warrant - targeting reporters Dan Oakes and Sam Clark as well as news director Gaven Morris - allowed the AFP "to not just take and seize but to delete and to change official ABC documents", Mr Lyons told ABC TV.
The ABC assisted forensic digital officers in sorting through the material but could yet refuse to hand over any documents and instead contest the warrant in court.
The ABC's lawyers took out many documents on the basis of legal privilege, Mr Lyons posted on Twitter.
AFP officers left the ABC's Ultimo offices by just after 8.30pm on Wednesday after both parties agreed to a two-week hiatus.
During this time, any documents which are handed over under the warrant can be challenged, or the entire warrant can be challenged, Lyons posted.
The ABC and AFP agreed on documents which fit the warrant.
These were sealed and the AFP is not allowed to open the documents for two weeks, which gives the ABC "time to challenge," Mr Lyons posted.