Prime Minister John Key says State Services Commissioner Iain Rennie, not the Government, instigated the hunt for the people who leaked Cabinet papers.
The Government wants to track down those responsible for leaking papers about mining in high-value conservation areas and proposed changes to the state sector.
Despite a spokesperson for Mr Rennie saying ministers asked for the investigation and State Services Minister Tony Ryall's office saying Mr Ryall ordered it after Cabinet discussed the matter, Mr Key insists Mr Rennie initiated it.
Mr Key says it is up to the commissioner to decide whether to investigate any substantial breach.
The investigation follows claims by Forest and Bird that Cabinet is considering opening up 7000 hectares of prime conservation land to mining - a suggestion Mr Key has said he would not dignify with a response.
Another leak resulted in media reports about potential mergers in the state sector.
Earlier, Mr Ryall said he ordered investigations into both leaks, adding that he took the unauthorised disclosure of government information very seriously.
In a statement, Mr Rennie said the unauthorised release of Government information had the potential to seriously undermine trust in the public service.
Mr Rennie says he would have initiated an investigation even if Mr Ryall had not asked him to do so.
Mr Rennie says police may be called in to look at staff computers in order to review documents and emails. He expects the probe to take several weeks.
But Mr Key insists the commissioner instigated the inquiry.
The Green Party says holding an inquiry to try to find the people responsible for leaking cabinet papers is completely over the top.
Co-leader, Russel Norman, says the inquiry is clearly aimed at stopping anyone telling the public what the Government's secret plans are, and if the Government wasn't so secretive, such leaks wouldn't occur.
Labour's state services spokesperson, Grant Robertson, says the Government is overreacting.
"This looks like a witch hunt to me, by ministers, and I really think that they've got to look in the mirror when it comes to why these documents have found their way into the public arena," he says.
Mr Robertson says National has been secretive about its plans for mining on the conservation estate and has not consulted people involved in public sector agencies they want to merge, so it's no surprise someone has chosen to blow the whistle.
However Prime Minister John Key says the inquiry is not a witch hunt, and says it is appropriate to investigate when a serious breach happens.
"It is important if we can find where that leak came from, that helps to add to the overall integrity of the New Zealand state service."
Forest and Bird advocacy manager Kevin Hackwell says he did not see a Cabinet paper, but was briefed on it.
He says it cannot be assumed the information came from a departmental or ministerial official because there are all kinds of people involved in the development of such policies.