The Australian Workers Union (AWU) has vowed to do everything it can to try and take back documents seized by the Australian Federal Police (AFP).

The union’s Sydney and Melbourne offices were raided yesterday, as part of an investigation into donations made to GetUp and Labor candidates when Opposition Leader Bill Shorten was leading it.

The AWU will today head to the Federal Court in an attempt to stop the documents being examined by the Registered Organisations Commission (ROC).

In its application to the court, the AWU will object to the validity of the investigation and the warrants.

If successful, the commission could be banned from using the collected documents as part of their probe.

The ROC yesterday issued a statement saying it sought warrants to the Sydney and Melbourne offices because it was concerned documents relevant to the investigation were being tampered with.

The ROC investigation is examining whether a $100,000 donation made to activist group GetUp in the financial year ending 2006 abided by union rules.

“Since the investigation commenced, the ROC received information which raised reasonable grounds for suspecting that documents relevant to this investigation may be on the premises of the AWU … and that those documents may be being interfered with (by being concealed or destroyed),” the ROC said in a statement.

It is a claim unions have denied.

In response to the raids, Mr Shorten stopped short of criticising the Australian Federal Police, arguing they were simply doing their job, but claimed the government was conducting a political witch hunt against him.

“The Government is wasting taxpayer money in an increasingly grubby effort, by a grubby Government, and quite frankly a grubby Prime Minister,” he told media on Wednesday.

“I want to make this pledge to the Australian people – Turnbull can be as focused as he wants on smearing me. I’m focused on serving you.”

But Prime Minister Malcolm Turnbull called on Labor to apologise for insinuating the AFP is a political instrument.

“That shows the lack of respect the Labor party has for the AFP and the rule of law,” he said.

“The AFP are completely independent, as Labor knows and indeed as Mr Shorten has said on previous occasions – he knows that as well as all of us do.”

Employment Minister Michaelia Cash later said she was not aware of the AFP raids until they were undertaken.

Senator Cash told Senate estimates she received a call from the ROC once the search warrant was executed and shortly before she saw them on broadcast on television.

She has told Labor Senator Doug Cameron that she “literally watched it unfold on the television” herself and had not had discussions with the Employment Department or the ROC.

The Australian Council of Trade Unions secretary Sally McManus have instead accused the Federal Government of orchestrating the raids in an attempt to damage Mr Shorten.

“This is an outrageous abuse of power. It is an attack on democracy and it is massive overreach,” Ms McManus told the ABC’s 7.30 program.

“We should be very concerned in this country where a government goes about directing their police to raid union offices.”

Police are raiding the offices of the Australian Workers’ Union. Photo: ABC

But in a statement, a Government spokesman denied the claim.

“The AFP is completely independent of Government. It is absurd and false to suggest the AFP is in any way politicised,” the spokesman said.

Ms McManus said the AWU had nothing to hide.

“The AWU is not concerned one little bit, they believe everything is totally above board,” she said.

In a statement, GetUp said it had nothing to hide because the investigation was focused on union rules.

“GetUp has previously acknowledged receipt of a donation of $100,000 in the 2005-2006 financial year from the Australian Workers’ Union,” it said.

“GetUp handled that donation appropriately, and there is no suggestion otherwise.”

The other part of the investigation is looking at a $25,000 payment made by the AWU to Mr Shorten’s election campaign in the Melbourne seat of Maribyrnong in 2007, and another two payments to campaigns in the seats of Petrie (Queensland) and Stirling (WA).

Ms McManus said she did not understand what was wrong with workers donating money to a political campaign.

“That is called democracy … I am entirely confident everything is fine and the Australian people will find out this and everyone should be angry about the fact that resources have been used to raid union officers,” she said.