The 35-year-old Welsh frontman of the rock group appeared via video link at Cardiff Crown Court, reports BBC News.
The singer had already been remanded in custody on December 19, and had been scheduled to appear before court again today (December 31).
Watkins is currently being detained at Parc Prison, Bridgend and faces six charges, including conspiring to rape a child under the age of 13 and distributing child pornography.
Watkins reportedly wore a black suit, shirt and tie for the hearing. Defending barrister Tom Crowther had said on December 19 that Watkins would be denying the charges.
Two women aged 20 and 24, who cannot be named for legal reasons, are also being held for similar offences.
The Daily Mail additionally reports that all three defendants spoke only to confirm their names at the hearing, which lasted "less than 10 minutes". All three defendants were remanded until March 11.
Watkins has sold over 3.5 million records with Lostprophets.
The other members of the band, Jamie Oliver, Lee Gaze, Luke Johnson, Mike Lewis and Stuart Richardson, have posted a statement on their official website expressing their shock at the charges against Watkins.