Australian Federal Police (AFP) officers have raided the Brisbane office of the Construction, Forestry, Mining and Energy Union (CFMEU) at Bowen Hills.

In a statement, the AFP said the raid was part of an ongoing investigation, but would offer no further details.

Union employees told the ABC they had no idea why their office was being raided.

CFMEU national construction secretary Dave Noonan condemned the raid, saying more than 25 AFP officers arrived at the office at about 7:00am and executed a search warrant.

He suggested the raid was related to the Royal Commission into Trade Union Governance and Corruption, but questioned the need for it, saying the union had fully complied with all the commission's requests.

"We respect the important work of the police in protecting the community, but challenge the legitimacy of this operation, given that their resources could be better utilised elsewhere," he said.

"At a time when the world is on heightened terror alert, while our communities require protection from drug dealers and organised crime, it is a disgrace that scarce police resources are being wasted on attacking workers and unions.

"The same thing happened in Canberra and it is nothing but a show for the media. We have nothing to hide and have fully complied with our obligations to produce documents.

"The community have a right to know why their tax dollars are being spent in such a disgracefully partisan way."

One officer was seen leaving the building carrying a backpack and a folder, but declined to comment on the material seized.