The news comes amid reports TV executives at America's ABC network have scrapped a host of hit shows including Eli Stone and Dirty Sexy Money after a slump in ratings.
And although it has not been confirmed whether law comedy Eli Stone, which recently featured a cameo from Katie Holmes, and Dirty Sexy Money have been pulled, Fuller admits his show will no longer run on the small screen.
Pushing Daisies, starring British actress Anna Friel and American star Lee Pace, is about a pie-maker who has the power to bring the dead back to life. It premiered on the network in October 2007.
He tells E! Online, "(ABC president) Steve McPherson called me, and said 'We gave it the best shot we could'.
"It's very likely that Pushing Daisies will end after episode 13, which as you know, is a cliffhanger."
But Fuller, who also created the show, insists he isn't too upset about the move, because he has a lot of plans for the series away from the limits of TV.
He adds, "We are talking to DC Comics about doing comic books that will wrap up our storylines, and I already have a pitch for a movie ready to go.
"I'm really not feeling very boo-hoo about it. I am so proud of the show. We put together 22 really good episodes, and there is a lot to be proud of. I'm sure I'll be working with a lot of these people again, and I would love to do so."