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).

Key points: AWU Sydney and Melbourne offices were raided as part of an investigation into donations made to GetUp and Labor candidates

AWU Sydney and Melbourne offices were raided as part of an investigation into donations made to GetUp and Labor candidates The AWU will object to the validity of the investigation and the warrants

The AWU will object to the validity of the investigation and the warrants The Government has denied allegations it orchestrated the raids

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.

"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. The Opposition and 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. ( ABC News )

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.

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.

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.

Mr Shorten refused to comment on the raids.