The $915 million museum in western Sydney, billed as one of the world's most significant new museum projects, is set to open in November.
On Thursday Powerhouse chief executive Lisa Havilah stood aside, pending the investigation of fresh allegations regarding governance and procurement at the museum, the NSW government announced.
Allegations had been put to several Powerhouse executives as part of a serious misconduct investigation ahead of the institution's formal opening, NSW arts minister John Graham confirmed at a budget estimates hearing on Monday.
"The idea that two of the senior executives were working through this process, this detailed process, and could also make sure that went smoothly was really starting to become unsustainable," he said.
The museum's chief operating officer Mark Wilsdon is on leave and is providing significant information as part of the investigation, Mr Graham said.
Ms Havilah agreed to step aside following a conversation about further allegations that had come to light, department of creative industries secretary Melanie Hawyes told the hearing.
But she cautioned any interim leadership arrangement should not be interpreted as a sanction or finding.
"These allegations that have come to light need to be tested, and that is what this investigation will do," said Hawyes.
NSW government architect Abbie Galvin has been appointed interim chief executive and former Opera House chief executive Louise Herron has been appointed as a strategic advisor, with both to start their roles on Tuesday.
A separate NSW Treasury review of the museum's operational budget is separate to any allegations, Hawyes said.
Spending at the Powerhouse under Ms Havilah's leadership has included items such as a documentary on the building of the institution, to cost at least $1.7 million, about $5 million on marketing, and $333,500 on the interior design of on-site accommodation.
In response to a whistleblower complaint, an initial probe was launched in March 2025 and the state's anti-corruption commission was notified, while a formal misconduct investigation began last December.
The procurement deals in question were under about $6 million, the amount the chief executive is authorised to spend without ministerial approval, the hearing was told.
Mr Graham defended his handling of the controversial project, insisting that issues going back to at least 2023 had been dealt with appropriately.
The Powerhouse board members including chair of trustees David Borger were not subject to the the allegations, and the board's audit committee has assisted with investigations, Mr Graham confirmed.
The minister said he was confident the project, which he described as the Opera House of the west, would open to the public as scheduled on November 7.