Police in Melbourne have all but confirmed that a high-profile rape case against AFL St Kilda star Stephen Milne will never be prosecuted, with key evidence missing and officers embroiled in conflicts of interest.

Deputy Commissioner Graham Ashton could not explain why or how evidence, believed to be exhibits, could disappear during the 2004 investigation, but noted it was not a common occurrence.

"It would appear in this case, as I'm briefed, that there are areas that have got to be fixed up," he told reporters on Thursday, announcing that there would be a review of the file.

The decision came after Victoria's police watchdog, the Office of Police Integrity (OPI), recommended a review of the brief of evidence.

An OPI report into the matter found there were reasonable concerns among officers that the case was the subject of undue interference, a police statement said.

Mr Ashton revealed that conflicts of interest among his officers should have resulted in the case being handled differently.

"They had other social and professional relationships that meant that they shouldn't have been in a position to know what was happening in the investigation," he said.

The revelations may provide some level of vindication for Scott Gladman and Mike Smith, two former detectives who went public in 2010 with claims they had faced threats and intimidation from inside the force, and by powerful backers of the St Kilda club, to drop the investigation into the alleged rape of a 19-year-old woman.

Milne, who reached his 500-goal milestone last weekend, and fellow Saints player Leigh Montagna, were the subject of the police probe for two months in 2004, but both denied the allegations and were never charged.

St Kilda coach Scott Watters sought to distance the club from the ongoing issue as it re-emerged on Thursday.

"This is a police investigation into police procedure - it's not an investigation into St Kilda Football Club or any players and that distinction really needs to be made," he told SEN Radio.

Despite the fresh police review, to be conducted by the state's sex crimes squad, charges are not expected to ever be laid.

"From what I'm briefed, it's very unlikely, highly unlikely," Mr Ashton said, adding that it was "extremely unlikely" that anyone would be reinterviewed.

He said the review is primarily aimed at making sure the file is in appropriate shape.

Victoria Police noted in a statement that the force has "implemented substantial reforms and improvements to its sex crimes investigative processes" since the botched investigation.

But police corruption whistleblower Simon Illingworth said such statements are missing the point.

"The concerns raised by the police involved are not policy concerns; they are people concerns," he told AAP.

"They were worried that people were trying to alter the outcome of an investigation. There were already many policies in place against such behaviour, and especially against being able to remove evidence."

He hoped police would offer an apology to the alleged victim, who has seen her case drag on for eight years and may never lead to a prosecution.

Mr Ashton said the long delay is regrettable.

"If someone makes an allegation of a sexual offence it's a serious matter and should be properly investigated," he said.