Revelations that private investigator Glenn Mulcaire may have intercepted voicemail messages left by relatives for the 13-year-old on behalf of the Sunday tabloid triggered the phone hacking controversy that has shocked Britain.
The IPPC has now received a "voluntary referral" from Surrey Police regarding information that an officer in the force may have supplied the News of the World with details relating to the Dowler case. The schoolgirl was murdered by doorman Levi Bellfield in 2002.
The commission now intends to run its own independent investigation into the allegations and will write to the solicitor representing the Dowler family to inform them of the development.
In a statement, the IPPC said: "The IPCC has received a voluntary referral from Surrey Police regarding information they received alleging that a Surrey officer gave information to the News of the World in relation to the investigation into Milly Dowler's murder in 2002. A decision has been made that the IPCC will independently investigate.
"An IPCC deputy senior investigator has been over at Surrey Police this morning to get more information about the case and will be writing to the Dowlers' solicitor at the family's request.
"Until we have shared further detail with him it would not be appropriate for us to make it public."
The phone hacking scandal has prompted Rupert Murdoch's News Corporation to shut down the News of the World and withdraw its £8 billion-plus proposed takeover of Sky.
News Corporation chief executive Murdoch was said to be "humbled and shaken" as he apologised in person to the family of Milly Dowler last month over the alleged hacking of the schoolgirl's phone.
In an equally shocking revelation, it has since emerged that Sara Payne, whose 8-year-old daughter Sarah was murdered in July 2000, has been informed by police that the Sunday tabloid may have hacked her phone.