Gabriel Makhlouf will be investigated over his allegations of hacking in relation to Budget leaks.
Last week the outgoing Secretary to the Treasury publicly claimed there were "multiple and persistent" attempts to access classified Treasury information.
His statements came after National revealed details of the Government's Wellbeing Budget two days before it was officially released.
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Makhlouf told The AM Show there had been at least 2000 attempts to gain unauthorised access to Budget information and he had referred the issue to police.
However police later advised the Treasury that the leak seemed to be a result of someone exploiting the website search tool, which does not constitute hacking and is not unlawful.
Makhlouf has been roundly criticised for his comments, and Finance Minister Grant Robertson refused to express confidence in him on Friday.
Prime Minister Jacinda Ardern told media at her post-Cabinet press conference she expected Makhlouf's comments to be looked into.
On Tuesday the State Services Commissioner announced an investigation into Makhlouf's "actions and public statements" about the cause of the Budget leak.
"The investigation will establish the facts in relation to Mr Makhlouf's public statements about the causes of the unauthorised access; the advice he provided to his Minister at the time; his basis for making those statements and providing that advice; and the decision to refer the matter to the Police," a statement reads.
Commissioner Peter Hughes said questions of "considerable" public interest have arisen from Makhouf's actions.
"It's my job to get to the bottom of this and that's what I'm going to do," he said.
Deputy State Services Commissioner John Ombler QSO will lead the investigation, which will be done quickly - ideally before Makhlouf leaves for his new role at the Central Bank of Ireland on June 27.
The findings will be made public, as will the Commissioner's view of them.
"Mr Makhlouf believes that at all times he acted in good faith," Hughes said.
"Nonetheless, he and I agree that it is in everyone's interests that the facts are established before he leaves his role on 27 June if possible. Mr Makhlouf is happy to cooperate fully to achieve that. I ask people to step back and let this process be completed."
The investigation into Makhlouf is unrelated to the inquiry into the Budget leak itself, which was announced last week.