Garda Commissioner Martin Callinan has asked the High Court to prevent the release of thousands of documents relating to the killing of Sophie Toscan du Plantier, including a key internal report into how gardaí conducted the murder investigation.
The court recently ordered gardaí to hand over all relevant files to English-born journalist Ian Bailey.
He is suing the State amid claims that he was wrongly targeted by gardaí as part of their inquiry into the Frenchwoman's murder in west Cork in December 1996.
According to court documents seen by RTÉ's This Week programme, the Commissioner has asked the High Court to withhold an internal report carried out by Assistant Commissioner Ray McAndrew.
The Commissioner has also applied to withhold a series of recommendations that the senior garda made to the Director of Public Prosecutions in May 2007 arising from his report.
In total, Mr Callinan has asked the court to withhold 128 separate files containing 2,898 document pages of confidential information.
This includes 327 pages of the original garda investigation report.
It also includes three confidential reports authored by a senior garda, Chief Superintendent Tom Hayes, details of which have not been in the public domain before.
According to a list of items the Commissioner wants to keep under wraps, Chief Supt Hayes is listed as the author of a 147-page report drawn up last year that deals with concerns expressed in a secret report written by the State prosecutor's office in 2001 but which was only made public in 2011.
In that report, the DPP raised significant concerns about how gardaí handled the murder investigation, including allegations that a witness was offered drugs to incriminate Mr Bailey and that some gardaí launched a whispering campaign against him in west Cork, where he still lives.
Chief Supt Hayes is also listed as the author of another 42-page report relating to that male witness who was allegedly offered drugs to incriminate Mr Bailey.
Chief Supt Hayes is also identified as the author of an 111-page report itemised as the "Marie Farrell report", which is dated August 2012, and which the Commissioner also wants to withhold.
Ms Farrell was a witness who claimed she saw Mr Bailey near the scene of Ms Toscan du Plantier's murder in December 1996, but she later retracted her statement.
The DPP had also raised issue in relation to the second arrest of Jules Thomas, Mr Bailey's partner. The Commissioner has also applied to keep a significant amount of material relating to this arrest under wraps.
Meanwhile, it has also emerged that 25 original documents in relation to the murder investigation have gone missing, according to correspondence seen by RTÉ.
Of these, 24 are witness statements for which a typed memo exists but not the handwritten version.
The remaining missing document is described as the original suspect file for Mr Bailey and Ms Thomas. It is a single memorandum covering both individuals, and its whereabouts is unknown.
Mr Bailey's solicitor Frank Buttimer told RTÉ's This Week that his client was hoping to get answers to many questions in relation to how gardaí handled the murder inquiry, and that they would "certainly persist" in seeking the full release of all relevant material.
A spokesman for the Garda Commissioner said that Mr Callinan was entitled to assert privilege and seek legal advice where necessary, like any defendant in civil litigation.
He said the matter was currently before the High Court and he would not be making any further comment.