The chief executive of KPMG Australia has resigned after an investigation into the accounting giant's handling of a whistleblower's allegations.

KPMG chair Martin Sheppard has accepted the resignation of chief executive Andrew Yates effective immediately, the firm announced in a release today.

KPMG's national managing partner audit and assurange Julian McPherson will also stand down from his role effective immediately and will resign after transitioning his client responsibilities.

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The shake-up comes after legal firm Allens was appointed by the company to investigate its prior internal and external investigations, and found that they had fallen short of the rigour required to investigate a whistleblower's claim that client documents were being inappropriately shared internally.

"I have been committed to a speak-up culture in our firm, it is clear that in this case we have let ourselves down and I take accountability," Yates said.

Stan Stavros has been appointed interim chief executive.

KPMG is one of the "big four" global accounting firms, alongside Ernst&Young, Deloitte, and PwC.

"We apologise unreservedly to the whistleblower. We commit to learning from this process to ensure we create an environment where it is safe and easy to surface concerns that will be acted upon," Sheppard said.

"KPMG apologises to the clients whose information was not handled with the care and respect they expect from us. We also apologise to our people – as these matters do not reflect on the contribution they make to KPMG and our clients."

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Sheppard said Allens would continue to investigate the whistleblower's allegations, while KPMG has also engaged leading ethical organisational culture specialist Principia Advisory for a separate review into the firm's policies and processes to support people to speak up.

"KPMG is committed to transparency and will publish the findings of the Principia review. We will move swiftly to act upon their recommendations," Sheppard said.

"We are reinforcing and strengthening the controls that protect client confidentiality, and we will set out for our clients the specific steps we are taking to keep their information protected. For each of our audit clients we will confirm that any conduct matters do not impact the quality of their audits."

Sheppard said he knew KPMG would have to work on rebuilding trust.

"That's why we are not asking anyone to take our word for it, and we are inviting scrutiny and challenge on our remedial actions," he said.

The whistleblower's initial allegations about the inappropriate internal sharing of client information were not substantiated by an initial internal investigation or an external legal review of that investigation.

However, KPMG acknowledged that the initial investigation "was not conducted with the necessary rigour".

The whistleblower then approached several KPMG Australia board members, and "others", which prompted the Allens review.