An outside force has been brought in to investigate Fife Constabulary after two men who spent 10 years in jail had their murder convictions overturned.
Mr Allison and Mr Johnston had spent 10 years in jail
Steven Johnston, 42, and Billy Allison, 41, were found guilty of killing Drew Forsyth, 34, in Dunfermline in 1995.
But appeal judges said new evidence suggested a miscarriage of justice.
They ruled that officers "deliberately misled" the Crown by not passing on all the information they had about the date on which the victim was killed.
The Lord Justice Clerk, Lord Gill, said the police's conduct of the murder inquiry meant the men did not have a fair trial.
The investigation into Fife Constabulary will be carried out by Lothian and Borders Police.
Mr Forsyth was alleged to have died during a drunken row with Johnston and Allison on 3 November, 1995, although his body lay in his flat in Milton Green, Dunfermline, for another six days before it was found by his mother.
At least a dozen witnesses claimed to have seen Mr Forsyth, alive and well, in the days following the alleged murder date.
The appeal judges heard how they gave statements to police which then disappeared.
The information was not passed on to either prosecutors or defence lawyers.
Lord Gill said the Crown's case had depended on proving that the murder took place on 3 November 1995.
Johnston and Allison, who have always protested their innocence, were found guilty even though the defence led six witnesses who claimed to have seen the victim alive on later dates.
The case was eventually taken up by the Scottish Criminal Cases Review Commission after Johnston's lawyer pursued the question of whether police had not submitted evidence to the procurator fiscal.
Lord Gill said the appeal court had heard evidence from "credible and reliable" witnesses suggesting that Mr Forsyth was alive after 3 November.
The judges quashed the men's convictions after ruling that this evidence was so significant that the men had suffered a miscarriage of justice.
"The court has also heard extensive evidence relating to the conduct of the murder inquiry by officers of Fife Constabulary," said Lord Gill in his judgement.
"It has reached the conclusion that the police in this case suppressed evidence pointing to the deceased's having been alive after 3 November and altered certain statements, in one case on the crucial question of date of death."
He said the report submitted to the fiscal did not contain all of the evidence known to the police about the date of death.
"The court's final conclusion is that the police deliberately misled the Crown in a serious way and thereby induced the Crown to adopt the police theory of the date of the murder and to challenge the credibility and reliability of any defence witness who cast doubt on it," added Lord Gill.
However, he pointed out that the ruling was not a judgment on the guilt or innocence of Johnston and Allison.
A spokesperson for the Crown Office and Procurator Fiscal Service said: "We can confirm, in light of concerns raised during the course of the appeal, Crown Counsel have instructed that a full investigation be carried out into the gathering and reporting of information to the Crown by Fife Constabulary. "
A Fife Constabulary spokesman said: "We note the judgement in this case, and will take time to consider its terms carefully."