An ACT Supreme Court case brought by the Construction, Forestry, Mining and Electrical Union alleges the AFP raid and confiscation of information was unlawful.

The construction union has asked the court to impose an injunction to stop police from examining or using the seized material.

The CFMEU will then seek orders that the AFP return or destroy all the material seized during the search.

But ACT Policing says the search warrant was executed in "accordance with legislative requirements and established AFP protocols".

The application is expected to be heard on Thursday afternoon.

About 20 police attached to the trade unions royal commission swarmed the Dickson headquarters about 10.30am on August 26 in search of evidence of bribery and blackmail.

But police overstayed the warrant and were forced to execute a second about 9pm in order to continue the search.

In total, police stayed for about 13 hours, frisk searching all union officers and staff present, removing posters from walls, and going through the office safe and ceiling cavity.

The union says about 10,000 electronic and hard copy files, and mobile phones were seized.

The raid was prompted by evidence given to the trade unions royal commission during its Canberra sittings.

Court documents said the CFMEU had sought a judicial review of the decision of police to raid the offices and copy data, and the decision of Magistrate Beth Campbell to issue the second search warrant.

The union asked the court to restrain police from examining seized materials, and order the return of hard copies and the destruction of electronic data.

CFMEU Construction Division national secretary Dave Noonan said the raid on the ACT office had been unnecessary and unlawful.

Mr Noonan said the union had complied with numerous Royal Commission notices ordering it to produce documentation.

He said the royal commission could share this information with the police taskforce without resorting to raids.

"If the Royal Commission police taskforce wanted further material, the Royal Commission could have issued further notices rather than storming our office," Mr Noonan said.

"The police were at our office for nearly 13 hours and our staff assisted them by identifying documents and providing passwords and PINs.

"Yet despite all that, the police then obtained a second warrant to continue the search after 9pm on the basis that it was necessary 'to prevent the concealment, loss or destruction of property'."

Mr Noonan said the second warrant had been invalid because there had been no evidence to justify that finding.

He also said the union would allege that the AFP breached the requirements of the ACT Crimes Act in conducting the raid.

"The union has no tolerance for corruption in its ranks and has always made clear that corruption allegations should be investigated by the police who will have our full cooperation" Mr Noonan said.

"However the raid on our Canberra office and the charging of our organiser Johnny Lomax with 'blackmail' for getting members higher wages through an EBA are part of a coordinated campaign to use the police and criminal law against the union's legitimate and lawful industrial work on behalf of our members."

An ACT Policing statement said the search warrant had been obtained and executed legally and in line with internal protocols.

"The AFP taskforce attached to Trade Union Royal Commission governance is continuing its investigations," a police statement said.

"It would be inappropriate for the AFP to make any further comment whilst this matter is still in the investigation stage."

The raids followed criminal charges being laid against two men connected to the CFMEU ACT branch.

Former CFMEU organiser Kivalu was arrested and charged with two counts of blackmail after he told a royal commission he accepted payments of $60,000 from a Canberra formwork contractor.

Union organiser John Lomax is also facing a charge of blackmail.

Both men have pleaded not guilty.