Bill Shorten has attacked the federal police raids on Australian Workers’ Union offices in Melbourne and Sydney overnight, saying they were a new low for the Turnbull government.

“Yet again, yesterday, the government is wasting taxpayer money in an increasingly grubby effort, by a grubby government and, quite frankly, a grubby prime minister,” the federal Labor leader said on Wednesday.

“They have been exposed for standing for nothing and all they have left is to try to damage the reputation of their opponents.”

Daniel Walton, the national secretary of the AWU, has criticised the Registered Organisations Commission for asking the federal police to conduct the raids, saying the AWU would be making an application in the federal court on Wednesday for a return of the documents seized.

The AFP raided the union’s headquarters on Tuesday in support of an ROC investigation into donations the AWU made to the activist group GetUp when Shorten was in charge of the union.

The ROC received information that documents were being interfered with in the union’s offices “by being concealed or destroyed” while it was investigating whether the donations were within the union’s rules. It said a magistrate had authorised the AFP raids to seize the documents.

The employment minister, Michaelia Cash, this month referred the issue to the ROC after reports the union gave about $100,000 to the leftwing advocacy group when it launched in 2005.

Daniel Walton branded the raids “an extraordinary abuse of police resources” and said they were part of an attempt to smear Shorten.

He said the documents seized were more than 10 years old and “do nothing more than highlight the fact that the union made a few political donations”.

“We’re extremely concerned about the actions of the Registered Organisations Commission and extremely concerned of the actions of the Turnbull government,” Walton said on Tuesday.

On Tuesday GetUp said it had previously acknowledged receipt of a donation of $100,000 in 2005 from the AWU. “There is no suggestion of any impropriety on GetUp’s part on the receipt and handling of the donation,” a spokesman said.

The ROC website says an ongoing investigation into the AWU’s national office and the Victorian branch commenced on 20 October.

