The Independent Police Complaints Commission (IPCC) is investigating the conduct of the Deputy Chief Constable of Surrey Police Craig Denholm in relation to his alleged knowledge that Milly's mobile phone was illegally accessed by the News of the World in 2002.
He was the senior investigating officer for part of Operation Ruby, the Surrey Police investigation into the abduction.
The IPCC is also investigating the conduct of temporary Detective Superintendent Maria Woodall who was a Detective Chief Inspector and the senior investigating officer on Operation Ruby from 2006 onwards.
Surrey Police Authority voluntarily referred both officers.
The family of Milly Dowler is aware of the IPCC investigation.
In a statement, the Dowler family said: "The Dowler family welcomes the proper investigation of what happened at Surrey Police 10 years ago. They regret that the passage of time means that some individuals can now no longer be investigated. The family have no further comment to make at this time."
Operation Weeting, the criminal investigation by the Metropolitan Police Service into allegations of phone hacking, is ongoing and it would be inappropriate to comment any further at this stage.