A News Corp journalist at the centre of an Australian Federal Police raid on her house which was found to have been invalid by the High Court says the win is a "small victory" but not the end of the legal battle.

The warrant used by Australian Federal Police officers to search the home of journalist Annika Smethurst last year was thrown out by the High Court on Wednesday, but police will be allowed to keep the materials they seized in the raid.

Key points: The court found the warrant used to search Ms Smethurst's home was not correctly issued

The court found the warrant used to search Ms Smethurst's home was not correctly issued The saga sparked concerns over press freedom, but the court did not rule on that issue

The saga sparked concerns over press freedom, but the court did not rule on that issue Ms Smethurst's reports examined plans to expand spying powers

The court unanimously ruled the warrant was invalid but was split on whether police should be forced to hand back what they took.

Ms Smethurst's home was raided after the Sunday Telegraph published a story she wrote on plans to expand the powers of the Australian Signals Directorate (ASD).

The story included images of a document created by the ASD marked "secret" and "top secret", leading the AFP to argue Ms Smethurst and the Sunday Telegraph had broken the law by publishing them.

More than a year after the story went to print, the AFP obtained a search warrant for a range of general items belonging to Ms Smethurst and an order she provide her phone password.

The raid sparked a national debate about press freedom, which intensified when AFP officers searched the ABC's Sydney headquarters over a different story the same week.

The High Court unanimously found the warrant was invalid because it failed to specify the offence being investigated.

The court did not consider any other arguments on whether the raid had any impact on the implied freedom of political communication.

The court ordered the AFP pay the costs of Ms Smethurst and her employer News Corp.

Journalist Annika Smethurst says she never intended to become the poster girl for press freedom. ( ABC News )

Prosecution against Ms Smethurst not ruled out

Speaking after the decision, Ms Smethurst said the High Court's decision provided some relief but was one step on a long path ahead.

"I wrote this story nearly two years ago … and we've had an ongoing investigation, an ongoing legal fight, and really although it has been a small victory for me this is far from over," she said.

"It's really something that's been an ongoing stress for myself and for my loved ones and also a huge fight for the media industry and something we have to continue.

"Although we're a step closer today to resolving this, it really hasn't brought any closure for me."

Ms Smethurst said she had never intended to become the "poster girl" for press freedom but was glad her case had ignited discussion.

She said even though her stories were later confirmed when Home Affairs Minister Peter Dutton conceded there was a plan to expand the agency to target child sex offenders, it did not change the looming threat of charges against her in the future.

"Just because the story is correct it doesn't change the fact that prosecution has not been ruled out for myself or the two journalists at the ABC," she said.

"Until we have widespread reform there really is no assurance that we can have that we won't be prosecuted."

AFP Commissioner Reece Kershaw says Ms Smethurst's phone has been quarantined and cannot be accessed. ( ABC News: Tamara Penniket )

Data from phone quarantined, AFP Commissioner says

AFP Commissioner Reece Kershaw said he respected and accepted the High Court's judgement, and additional measures had been put in place since last year to ensure warrants were properly drafted.

Commissioner Kershaw said it was still unclear whether police could use data obtained from Ms Smethurst's phone during the search as evidence in future cases, including any brought against Ms Smethurst, related to the classified leak.

"What we'll do carefully and correctly is take legal advice, both probably from our in-house legal advice on what we do with that particular material," he said.

"At this moment, [the data] is quarantined. Investigators are not able to look at that."

Ms Smethurst said she was "disappointed" the High Court did not make an order that the data be destroyed or handed back.

The Commissioner was also quizzed about when there would be a resolution in the ongoing investigation into both Ms Smethurst and the ABC journalists at the centre of the Sydney headquarters raid.

"All of us want to see this resolved as expediently as possible," he said.

"We wanted to finish it earlier, noting we had to be respectful of both the court processes in the Federal Court and the High Court."

He said he believed the oversight board considering both investigations would have a decision within "weeks".

Case a 'sorry mess': News Corp

News Corp executive chairman Michael Miller said the case highlighted the need for news organisations to be allowed to challenge warrants against journalists.

"The Federal Police must obey the law, and their raid on Annika Smethurst's home was illegal," he said.

"The Federal Government must allow media organisations to contest warrants against journalists to avoid debacles like this one occurring again.

"It's time for the Federal Government to bring this sorry mess to a prompt end.

"It's time to end Annika's ordeal."

Lawyers for Ms Smethurst and News Corp argued the court should issue an injunction requiring the AFP to hand back the seized materials or destroy any copies.

While the court was unanimous in quashing the warrant, it was divided over what should happen to the material seized.

Political journalists campaign for the public's right to know outside Parliament House on 21 October 2019. ( ABC News: Toby Hunt )

The data taken from Ms Smethurst's phone was identified through specific word searches for items including mentions of the ASD and story pitches.

The Commonwealth had asked the High Court to find it should be allowed to keep the material, even if it was obtained illegally.

While three judges said they thought the material should not be kept by police, the majority of the court declined to make an order, meaning police could keep the material for any future possible prosecution related to the case.

The journalists' union, the Media Entertainment and Arts Alliance, issued a statement welcoming the decision, but raised concerns about the court allowing police to keep the documents.

If the case was ever to come to trial, lawyers could argue the data was not able to be used as evidence because the warrant had been thrown out by the highest legal authority in the land.

But no trial is on the horizon, and Attorney-General Christian Porter has said any decision on prosecuting journalists will need to be signed off by him.

A spokesman for the AFP said it was considering the decision and would "act in accordance with the ruling".