Victoria Police assistant commissioner Steve Fontana said on Wednesday a more detailed brief had been handed to the Director of Public Prosecutions after the review was completed.
However, the OPI found there was no evidence of "interference" when it came to the original brief.
"On the basis of advice received, charges have been laid," Fontana said.
Milne, 33, faces four charges related to an alleged incident in 2004.
Fontana said the original brief had been 'incomplete' in gathering witness statements, so further investigation had been ordered.
"Last year the OPI returned the brief of evidence to Victoria Police with the recommendation that we actually review it to make sure that all the appropriate evidence is attached to it so it could be put away," he said.
"We handed that job to the sex crimes squad, who are specialists in investigating these types of offences.
"Whilst they were going through this particular brief of evidence, they found it was probably inadequate, is the best way to describe it.
"We spoke to the alleged victim in this matter to see if she still wanted to proceed, and after speaking to the victim we commenced to conduct further enquiries in relation to this matter."
The OPI found there was "no evidence of interference in this particular matter".
"During the review of the brief, we've certainly found that as well. We've got no evidence to suggest there has been interference but we have got concerns about the standard and the way in which the investigation was conducted," Fontana said.
"We are recommending that that be looked at a little bit more closely."
Fontana said there was disappointment with how the initial investigation was handled and that the detectives involved were not specifically trained.
He also said Victoria Police had "come a long way" since.
"It doesn't really help the delay in this matter, the victim, nor the persons charged," he said.
"Bearing in mind this was conducted by a local criminal investigation unit; yes, they are trained as detectives but they're not specialist investigators.
"Since that time, Victoria Police has invested a lot of resources in building our capability into investigating sex offences.
"We've got a network of units throughout the state that have specialist skills in the investigation of sex offences."
Fontana believed two of the detectives involved in the initial investigation had left Victoria Police since.
He said measures were in place to ensure the same thing didn't happen again and members were expected to disclose personal conflicts in investigations.
He also hoped this example didn't discourage victims of sexual assault to come forward in the future.
"It's unfortunate what's happened and we are sorry about this. No one likes to see a substandard investigation. It doesn't do anyone good, whether you're the alleged offender in the matter or the victim," he said.
"This is a serious offence and to be quite honest, particularly the victims in this case deserve better but also it's distressing for a long period for the offenders or the accused in these matters.
"We really do have good practices, we've got really skilled investigators throughout the state and we do have place a lot of emphasis on the support for victims."