"The CFMEU confirms that AFP and NSW Police have served a search warrant at the NSW branch office in Pyrmont and at private premises," Mr Noonan said.
"The union is co-operating to the extent required by law."
The AFP said earlier the raids related to an ongoing Trade Union Taskforce investigation.
Mr Noonan noted the raids follow similar occurrences at other CFMEU offices across the country.
"The AFP have been taking an increasingly active role in industrial relations matters, and have previously raided CFMEU offices in Canberra and Brisbane," he said.
"Neither of those raids resulted in any charges being laid against any union official.
"In the case of Canberra, the AFP actions were found to be unlawful by the ACT Supreme Court."
The AFP said the raids were ongoing it could provide no further information at this time.
The national union represents about 180,000 workers.
The NSW branch is currently preparing for the election of officials, including its state president, with a ballot due to open in January.
In 2014, the Australian government established a joint police task force to investigate conduct uncovered by the Royal Commission into Trade Union Governance and Corruption.
The taskforce is co-ordinated by the AFP in conjunction with state police teams.