The 36-year-old singer with Lostprophets is to be sentenced next month after admitting a string of sex offences including attempted rape of a baby.
The Independent Police Complaints Commission (IPCC) has now announced it is investigating the handling of a complaint made against Watkins in 2012 to South Yorkshire Police.
The watchdog, which has already opened an investigation into whether South Wales Police failed to act quickly enough, said the inquiry followed a referral from the force in September.
In a last-minute change of plea on Tuesday ahead of what would have been his trial at Cardiff Crown Court, Watkins admitting sexually touching a one-year-old and encouraging a groupie to abuse her own child during a webcam chat.
The singer, from Pontypridd, south Wales, also admitted possessing and making child porn as well as launching the plot to rape a baby.
A spokeswoman for South Yorkshire Police confirmed the force had referred itself to the IPCC but said: “To ensure the integrity of the IPCC investigation, the Force is unable to add further comment at this stage.”
Watkins’ ex-Lostprophets band-mates have insisted they did not know about the abuse. Speaking for the first time since his plea on Tuesday, they revealed in a statement that they were “heartbroken, angry and disgusted”.