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The Whale Oil blogger's complaint about the hacker called Rawshark went directly to Assistant Commissioner Malcolm Burgess, according to documents obtained by the Scoop news agency.
The documents include an affidavit in which a former Counties-Manukau police officer raised questions over the level of energy dedicated to the hacking of Slater's computer.
Former police area controller Wayne Stringer said: "I am very surprised to see how much effort and police resource has been devoted to this case. The Counties-Manukau office routinely deals with large volumes of very serious crime, including murders, rapes and crimes of violence and child abuse.
"Police have limited resources, and in my view rightly prioritise these crimes."
The documents detail the close involvement of Mr Burgess in the investigation.
Slater was overseas when he complained to Mr Burgess on August 19 in an email headed, "Complaint about illegal hacking and publication of private emails".
The court documents show Mr Burgess assigned the complaint to the National Criminal Investigation Group, who began work on finding Rawshark.
Emails show detectives at national headquarters were reassigned from organised crime to preliminary inquiries while the head of the police cyber crime unit assured Mr Burgess he would "have our best tech look at the possibilities and get back to you".
By August 28, when Slater walked into Counties Manukau police station to make a formal complaint, the draft investigation plan had been developed by the NCIG and the head of the cyber crime unit was giving advice to the crime manager at Counties Manukau on what to ask Slater.
The material included a letter from police to Dirty Politics author Nicky Hager's lawyers which showed Mr Burgess was briefed before the search on Hager's house and "endorsed" the application for a search warrant.
A spokesman for police headquarters said it was not unusual for national headquarters staff to be sent complaints.
The spokesman said Mr Burgess passed the complaint to the NCIG at headquarters "which at the time was already coordinating a number of matters arising from the publication of the Dirty Politics book".
The NCIG took a number of steps "to assist the district" including the draft investigation plan. The final plan was written by Counties Manukau staff. He said there was nothing unusual in detectives at headquarters helping district staff with issues that involved significant public interest.
- By David Fisher of the New Zealand Herald
* David Fisher gave evidence as an "expert witness" in the Hager v Police case under High Court rules that require an "overriding duty to assist the court impartially on relevant matters".