The Avengers director told Entertainment Weekly that a follow-up to his 2008 online musical - which starred Neil Patrick Harris - is still in the works.
"We really want to shoot it [in 2013]," he said. "We feel strong about the idea and we have a bunch of stuff written."
However, Whedon explained that starting work on the project is dependent on his busy schedule, since he is also developing a sequel to The Avengers and working on ABC's S.H.I.E.L.D. series.
"I have a certain bandwidth issue I am trying to overcome," he quipped.
Nathan Fillion - who played Captain Hammer in Dr Horrible - told Digital Spy in July last year that he expected a sequel to emerge in the near future, while Big Bang Theory actor Simon Helberg - who played henchman Moist - also told DS that he is "excited" for the project.
The original Dr Horrible received its television debut on October 9, 2012 on The CW, edited down to 42 minutes to fit the one-hour time slot.
> Dr Horrible sequel to shoot in 2013?
Watch a clip from Dr Horrible's Sing-Along Blog below: