The 75-year-old retired Pukekawa farmer dismissed a police review of the original investigation, due to be released soon, as a mockery after the funeral comments - where mourners heard Mr Hutton was known for having "integrity beyond reproach".
"We have a police system now that doesn't want to look at who done it," Mr Thomas said. "Oh no, we have a police system now that is protecting their own."
Mr Thomas, supported by daughter Bridgette and brothers Ray and Des at a press conference, accused Mr Hutton of criminalising the police force and said he and Mr Johnston were corrupt.
He wanted police to find the real killer and apologise to him [Mr Thomas], but he did not believe either would happen.
"It's a blatant cover-up. They have to admit that they fabricated evidence and apologise to me in writing."
Des Thomas said the Court of Appeal upheld the finding that Mr Hutton and Mr Johnston planted a gun shell casing, which framed his brother.
Ray Thomas claimed at least 10 other police officers had perverted the course of justice during the original investigation and they should also be held accountable.
However, at the funeral, Mr Bush said it was appropriate to recognise the service Mr Hutton gave to police from the comments made in his file which dated back to 1956.
Police do not accept the comments in any way had any connection with the review.
Mr Marshall said it was regrettable that the eulogy was being used to question the integrity of the review. He said Mr Bush attended the funeral at the request of the Hutton family.
"This was a difficult situation which required police to balance its obligations to the grieving family of a former member against the wider context."
The police presence at Mr Hutton's funeral had no bearing on the review, which was established in October 2010 after questions raised by Rochelle Crewe, the dead couple's daughter who was a toddler at the time of their killing.
He said the review, which would be independently assessed by Queens Counsel David Jones, involved 90,000 pages of documents dating back more than 40 years.
Detective Superintendent Andy Lovelock, who is heading the police review, said it was a work in progress.