A Federal Court judge has ruled an investigation by the union regulator into donations made by the Australian Workers' Union (AWU) to the activist group GetUp! in 2006 was invalid.

Key points: The judge found the basis upon which the investigation was launched was "flawed"

The judge found the basis upon which the investigation was launched was "flawed" But he rejected the union's claim that the probe had been carried out for an "improper political purpose"

But he rejected the union's claim that the probe had been carried out for an "improper political purpose" He said further hearings were needed to determine whether documents seized during raids on union offices should be returned

But Justice Mordecai Bromberg determined the Registered Organisations Commission (ROC) investigation into the donations, made when former opposition leader Bill Shorten headed the union, was not politically motivated as was argued by the union in a civil trial.

In October 2017, the Australian Federal Police raided the union's offices in Melbourne and Sydney, seizing documents related to union processes in approving the donations.

The raids were filmed by media agencies who were tipped off by the office of then-jobs minister Michaelia Cash.

The AWU mounted a legal challenge at the time, preventing the documents from being accessed.

Senator Michaelia Cash initially denied her office was involved in the raids. ( AAP: David Crosling )

Today, Justice Bromberg said further hearings were necessary to determine whether the search warrants were invalid.

Justice Bromberg said the basis upon which ROC executive director Chris Enright decided to conduct the investigation was "flawed".

He said that if after four years an alleged contravention of union rules had not been acted upon it was "deemed to have been in compliance" with the rules.

BIll Shorten led the AWU from 2001 to 2007. ( AAP: Dale Cumming )

The judge rejected claims by the union that the ROC investigation was done for an "improper political purpose".

"I have concluded that the evidence before the court does not establish that the decision made to conduct the investigation was made for the improper purpose contended for by the AWU," Justice Bromberg said.

Shorten rejects investigation as 'witch-hunt'

AWU national secretary Daniel Walton welcomed the court's ruling.

Key dates May 2017: Registered Organisations Commission (ROC) is established

Registered Organisations Commission (ROC) is established August 15, 2017: Senator Cash sends letter of referral to ROC outlining her concerns about a potential AWU breach of rules by donating $100,000 to GetUp!, after article in The Australian newspaper on the issue is published on August 1

Senator Cash sends letter of referral to ROC outlining her concerns about a potential AWU breach of rules by donating $100,000 to GetUp!, after article in The Australian newspaper on the issue is published on August 1 August 17, 2017: Senator Cash sends second letter of referral to ROC regarding $25,000 donation from AWU in 2006 to Bill Shorten's election campaign

Senator Cash sends second letter of referral to ROC regarding $25,000 donation from AWU in 2006 to Bill Shorten's election campaign October 20, 2017: ROC begins first investigation into 2006 AWU donations

ROC begins first investigation into 2006 AWU donations October 24, 2017, 9:30am: Magistrate approves AFP search warrants

Magistrate approves AFP search warrants October 24, 2017, between 12:00pm and 4:00pm: Senator Cash's media advisor David De Garis learns of imminent raids from Senator Cash's chief of staff, Ben Davies

Senator Cash's media advisor David De Garis learns of imminent raids from Senator Cash's chief of staff, Ben Davies October 24, 2017, 4:00pm: Media made aware by Mr De Garis and Michael Tetlow from then justice minister Michael Keenan's office

Media made aware by Mr De Garis and Michael Tetlow from then justice minister Michael Keenan's office October 24, 2017, 4:30pm: Media present as raids occur in Sydney and Melbourne at AWU offices

Media present as raids occur in Sydney and Melbourne at AWU offices October 25, 2017: AWU mounts challenge to raids and ROC investigation, AFP is ordered not to use the documents seized

AWU mounts challenge to raids and ROC investigation, AFP is ordered not to use the documents seized October 25, 2017: Senator Cash appears in Senate Estimates and initially states her office did not tip off media, but later corrects the record after learning of Mr De Garis's actions

"We were determined to bring the facts in this case to light, and that has taken a huge effort," he said in a statement.

"This has been an exhausting, resource-draining, and distracting process for our union, but it's a vital part of democracy that the actions of public agencies can and should be held to account."

Outside court, the union's lawyer, Josh Bornstein, said the ruling was "a big setback for Michaelia Cash".

A spokesman for Senator Cash said the Minister had been "cleared" by the ruling.

"The AWU's pursuit of the Minister was always a political game," the spokesman said in a statement.

"Despite the political attack by the AWU, the Minister has been cleared of any political influence over the ROC's decision."

In a statement acknowledging the ruling, an ROC spokesperson noted the AWU had "failed to demonstrate its allegations that the investigation had been commenced for any improper or political purpose".

The ROC was established in May 2017 and was billed as working to increase financial transparency in unions and employers associations.

The controversial legislation to introduce the regulator only passed with the support of two crossbench senators.

Mr Shorten said the investigation was "a waste of taxpayer money".

"This witch-hunt cost millions and the government cowboys running it did not even stop to check it their investigation was legal," he said in a statement.

Shadow Industrial Relations Minister Tony Burke said the court's decision had "shredded" the ROC of credibility and called for it to be shut down.

Read a summary of Justice Mordecai Bromberg's ruling:

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