Commissioner Paul Brereton has come under fire for his connection to the Australian Defence Force.
The army reserve major general has continued to consult with the defence force's watchdog after he led a landmark review into allegations of Australian special forces soldiers committing war crimes in Afghanistan.
National Anti-Corruption Commission inspector Gail Furness, who acts as its watchdog, revealed she received four complaints regarding a potential conflict of interest due to his defence force engagement, in an annual report tabled in parliament on Thursday.
One was resolved and a second was dismissed, while two remain under investigation.
Ms Furness previously concluded Mr Brereton had engaged in officer misconduct, which was when the act was not unlawful but was a mistake of law or fact.
She received 75 complaints about the watchdog in 2024/25, up from 50 the previous year, the annual report revealed.
Fifty complaints were about a decision not to investigate a person's referral.
The national anti-corruption commission has announced Mr Brereton would recuse himself from all defence-related matters in its October monthly report.
The commission said he had declared and appropriately managed any perceived or actual conflicts of interest relating to Defence referrals.
But media coverage of the issue had become a distraction to the commission's work and, Mr Brereton will recuse himself from all defence force-related matters, and not just units or people he had an association with, it said.
"Relinquishing those connections would not remove the potential for conflicts to arise, because of the historic relationships," the commission noted.
The commission said Defence only represented three per cent of referrals, which could easily be covered by its three deputy commissioners.
Independent senator David Pocock has called for Mr Brereton to step aside to restore trust in the anti-corruption watchdog.
The anti-corruption commission has 38 corruption investigations underway, 32 preliminary investigations, 11 joint corruption investigations with other bodies and three matters before the courts as of November 5.
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