The Australian Federal Police (AFP) have rushed to conduct raids on the Australian Workers' Union offices, amid concerns documents could be destroyed.

The raids are part of an investigation into payments made when Opposition Leader Bill Shorten was secretary.

Key points: The AFP says the raids were on behalf of the Registered Organisations Committee, an independent regulator for unions

The AFP says the raids were on behalf of the Registered Organisations Committee, an independent regulator for unions The investigation relates to whether donations made to activist group GetUp were authorised under union rules

The investigation relates to whether donations made to activist group GetUp were authorised under union rules It comes after the AEC asked GetUp to outline what funding it receives and how it is spent

The AFP issued a statement confirming it was carrying out the raids in Melbourne and Sydney on behalf of the Registered Organisations Commission (ROC), the independent regulator of unions and employer associations.

The investigation relates to whether donations made to activist group GetUp and to federal Labor campaigns were authorised under union rules.

In a statement, the ROC confirmed it launched the sudden raids because it was concerned evidence could be "concealed or destroyed".

"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 ABC understands the payments under investigation include $100,000 paid by the AWU National Office to GetUp in 2006.

Another is a $25,000 payment by the AWU National Office to Bill Shorten's election campaign in the Melbourne seat of Maribyrnong in 2007, and two other payments to campaigns in the seats of Petrie (Queensland) and Stirling (WA).

The AWU's National Secretary Daniel Walton described the raids as an "extraordinary abuse of police resources" by the ROC and the Federal Government.

"It is clear the ROC has been established not to promote good governance, but to use taxpayer and police resources to muckrake through historic documents in an attempt to find anything that might smear a future Labor PM," he told the ABC in a statement.

"This is a shameful new low for a Government already scraping the bottom of the political barrel."

Police are raiding the offices of the Australian Workers' Union. ( ABC News )

Federal Labor has alleged the raids are a "witch hunt", and has alleged Coalition interference.

"Malcolm Turnbull, when he's under pressure, calls the police," Shadow Employment Minister Brendan O'Connor told reporters in Parliament House.

"Today we learnt in Senate estimates there are resource issues with the Australian Federal Police.

"At the same time that that was uncovered, we have a situation where the Government is treating the police as its plaything — using the police to investigate a civil matter, an allegation that was made 10 years ago."

A spokesman for the Federal Government argued the AFP is "completely independent of government".

"It is absurd and false to suggest the AFP is in any way politicised," he said.

"Labor is attacking the independence, integrity and professionalism of the AFP and its officers. This is an offensive slur and a disgraceful distraction.

"This matter was referred to the Registered Organisations Commission weeks ago and it is important it is allowed to investigate without hysterical smears from Labor."

.Federal police officers arrive at the Victorian branch of the AWU in Melbourne. ( AAP: Julian Smith )

Separately, the Australian Electoral Commission (AEC) has asked GetUp to abide by disclosure laws that would require it to outline what funding it receives and how it is spent.

Groups subjected to such obligations are known as "associated entities", which are defined as a group controlled by one or more political parties, or operating to a significant extent for the benefit of political parties.

In a letter obtained by the ABC, the AEC said there were grounds to suggest GetUp's activities last year could be seen as having benefited Labor and the Greens.

GetUp has denied the claims and insisted it is an independent movement.