Mr Hutton and one other officer were singled out in the royal commission over a cartridge case said to have come from Mr Thomas' rifle and used to convict him of murder.
The commission, which concluded there was never any solid reason to charge Arthur Thomas, stated: "Mr Hutton and Mr (Len) Johnston planted the shell case ... in the Crewe garden and they did so to manufacture evidence that Mr Thomas' rifle had been used for the killings."
The Solicitor-General of the time, Paul Neazor, QC, told police there was not enough information to lay charges against Mr Hutton and Mr Johnston, who has since died.
Des Thomas spent four months building the file, specifying allegations against Mr Hutton based on sections of the Crimes Act, the law which police use to establish evidence and prosecutions of crime.
The claims do not directly deal with the cartridge case claims and subsequent finding by the commission.
Instead, Des Thomas has focused on steps taken by police to build the case against Arthur Thomas. One complaint cites section 115 of the Crimes Act, which carries a maximum sentence of 14 years in prison for anyone who "conspires to prosecute any person for any alleged offence knowing that person to be innocent".
The section of the act is contrasted against the Royal Commission's statement that "the police did not have just cause to suspect" Arthur Thomas had murdered the Crewes. "His arrest and prosecution for their murders was not justified."
Des Thomas has included affidavits supporting the claims from one of his other brothers, Richard Thomas. He said Arthur Thomas was not involved in the complaint, believing the nine years spent in prison meant life now had to be focused on the future rather than the past.
"He doesn't want anything to do with it."
The file was sent to police commissioner Peter Marshall on October 20 with a letter requesting a criminal investigation.
Mr Thomas said his complaint to police was independent of the review by Detective Superintendent Andy Lovelock, which was launched in 2010 after the Crewes' daughter Rochelle asked for a fresh inquiry into the murder of her parents.
Mr Hutton said he did not want to comment. "I've got nothing to say about what Thomas has said."
The pressure on police to respond to questions over the Crewe case led to the appointment two years ago of Mr Lovelock to review the murder inquiry. Along with the request by Ms Crewe, Arthur Thomas' former wife Vivien Harrison sought an independent inquiry into the case, after years of being labelled as the "mystery woman" who fed Rochelle in the days after she was left alone in the Crewes' Waikato home after their murders.
Police chief media adviser Grant Ogilvie confirmed receipt of the file.
"This is currently being assessed."