Federal police advised the justice minister's office just before warrants were executed on union offices, but the AFP chief says proper processes were followed.
Justice Minister Michael Keenan's office was advised by federal police just before search warrants were executed at two Australian Workers Union offices on Tuesday.
Mr Keenan told AAP on Thursday it was usual practice for such advice to be received.
"The AFP advised my office of the intention to execute search warrants immediately prior to them being executed, as is usual practice," Mr Keenan said.
The minister was briefed shortly afterwards, as was Prime Minister Malcolm Turnbull.
"Again, in line with usual practice, my office briefed the prime minister's office as the search warrants were being executed," Mr Keenan said.
The comment came as Australian Federal Police commissioner Andrew Colvin rejected claims his officers had been used as political pawns.
The AFP has come under scrutiny after officers executed the warrants in Sydney and Melbourne on Tuesday, as part of a bid by a Registered Organisations Commission to secure documents from tampering or destruction.
The ROC is investigating $200,000 in donations made by the AWU, including $100,000 given to activist group GetUp in the 2005/06 financial year while Bill Shorten was the union's secretary.
"The AFP makes all its operational decisions independently, based on experience, operational priorities and the law," Mr Colvin said in a statement.
"The AFP's primary obligations are to ensure the safety and security of the Australian community and enforce the rule of law.
"The AFP prides itself on its independence and integrity, and has a proven track record of these values while operating under the remit of eight individual prime ministers and their governments since it was founded in 1979."
Mr Colvin said the AFP had no operational reason to decline to execute a search warrant authorised by a magistrate.
He was also critical of reports which inflated the number of officers involved.
Eight AFP members were involved in the Melbourne search and five in Sydney.
AFP officers ordered media crews at the Sydney AWU office to leave, telling them they were hindering the investigation.