The charges follow a police review into an incident that allegedly happened in 2004.
The AFL is waiting for more information before it makes comment but CEO Andrew Demetriou said in statement that the charges were serious ones.
Demetriou said the AFL has asked for more information from the club.
Hesaid it was now vital to respect the legal process and the rights ofall parties, without ongoing speculation and commentary.
Milne, 33, was investigated after the alleged rape of a 19-year-old girl in 2004.
He has consistently denied the reports and had not been previously charged.
The original investigation was reviewed after the detective leading the investigation suggested he had dropped the charges in part because of pressure from other officers.
It has been reported that a senior officer linked to the case had a part-time job with St Kilda at the time.
St Kilda has confirmed that Milne was charged and said in a statement that the club would comment on Wednesday.
The statement said the club was "gathering details of this reinvestigation'.
A Victoria police spokesperson said on Tuesday: "Police can confirm that it has today charged a 33 year-old man from Cheltenham with four counts of rape following an alleged incident in 2004.
"He will appear in Melbourne Magistrates Court on 5 July, 2013.
"The decision to charge follows an extensive review of the initial investigation by specialist detectives within our Sexual Crimes Squad.
"That review was prompted by an OPI recommendation last year that the brief of evidence be reviewed to ensure all relevant evidence had been properly recorded and retained.
"As we have previously made clear, it is a matter of regret that this review found the initial investigation to have been substantially inadequate.
"As a result, further inquiries have been conducted by the Sexual Crimes Squad and after consulting with the Office of Public Prosecutions, the decision has been made to lay charges
"In recent years Victoria Police have implemented substantial reforms and improvements to our sex crimes investigative processes which has enabled a number of older investigations to be reviewed, offenders identified and charges laid.
"It is unfortunate for all parties concerned that this matter has taken so many years to progress, but having discussed with the alleged victim in this matter, we can confirm that our decision to lay charges accords with her wishes.
"It is now important that the defendant in this matter be afforded the same procedural fairness any other member of the community would expect in these circumstances.
"Victoria Police will be providing no further comment at this time and until the matter has run its course through the normal legal process.