The WA government-owned corporation is being audited by AUSTRAC, having acknowledged instances of historical non-compliance with anti-money laundering and counter-terrorism financing obligations.
It is also facing scrutiny over revelations it alloyed gold it sold to China with the addition of silver to save money between 2018 and 2021.
An investigation by the ABC's Four Corners program found the Shanghai Gold Exchange had raised complaints about two gold bars that did not meet its strict specifications.
Chief executive Jason Waters has said all of the gold bars exceeded the minimum 99.99 per cent industry standard, but the breach of the Shanghai rules relating to silver content was "unacceptable".
In his first public comments on the matter, long-serving chairman Sam Walsh conceded the revelations had damaged Perth Mint's reputation.
The former Rio Tinto chief executive said the mint had a "fully-aligned" leadership after a shake-up of the board and management in recent years.
"We acknowledge our historical shortcomings and non-compliances and are committed to learning from past mistakes," he told reporters on Tuesday.
"It takes time, and we have some way to go, but the Perth Mint is making good progress."
Mr Walsh said the mint was being "totally transparent" with AUSTRAC and had self-reported historical non-compliance issues.
He said the doping issue had been resolved to the Shanghai exchange's satisfaction before it was brought to the board in September 2021.
"Perth Mint is a very complex business with a lot of moving parts," he said.
"I would not expect that the board would be advised of every single issue that goes on in the daily operations."
An internal report had raised concerns, since downplayed by the McGowan government, that "up to 100 tonnes of stock" worth billions of dollars could be recalled to Perth to be recast at taxpayers' expense.
Mines Minister Bill Johnston said the government had inherited issues with the mint upon coming to office in 2017 but had since embarked on a reform program.
"So far as I am aware, no one has alleged there is currently money laundering at the Perth Mint," he said.
A strategic review which will examine whether the mint should remain under government ownership is due to be finalised later this year.
Mr Johnston said the outcomes of the review would be made public but the review itself would remain confidential for commercial reasons.
Perth Mint is Australia's biggest gold refinery with a turnover of almost $22 billion last financial year.
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