Two Victorian Building Authority (VBA) employees have been charged with criminal offences by the state's corruption watchdog over alleged bribes relating to building registrations.

On Wednesday, the Independent Broad-based Anti-corruption Commission (IBAC) conducted searches at a number of premises under warrant, resulting in the charges.

"These actions against key persons of interest are a result of IBAC's Operation Perseus — an investigation into allegations of corrupt conduct related to the assessment of builder registrations, in exchange for a financial benefit," an IBAC spokesperson said.

The VBA regulates the state's building and plumbing industries.

VBA commissioner and chief executive, Anna Cronin, said the authority had referred suspicious activity to IBAC in June last year and had been supporting their investigations since.

"Today IBAC notified us they have charged two employees with criminal offences and are now investigating a third," Ms Cronin said.

She said the employees involved had been stood down immediately.

"The VBA is now reviewing any impacts of this alleged activity to ensure the integrity of our systems," she said.

"We will not be commenting any further while the IBAC investigation and court processes are ongoing."

In March, the Victorian government announced the VBA's board would be replaced by a sole commissioner, Ms Cronin.

Minister for Planning Sonya Kilkenny in March said Ms Cronin had been leading major changes to the regulator's performance and culture, including ensuring consumer protection was at its core.