BBC Three has decided not to show a cartoon set in a fictional Vatican over concerns it would offend Catholics.
Stuart Murphy said it had been difficult to make the decision
The channel's controller said the comic impact of Popetown did "not outweigh the potential offence it will cause".
"There is a fine judgement line in comedy between the scurrilously funny and the offensive," Stuart Murphy said.
The BBC said it might recoup some costs through broadcast and video sales by BBC Worldwide and the series' creator, independent production firm Channel X.
Mr Murphy said shelving the ten episodes of Popetown had been an "extremely difficult and complex" decision to make.
"I knew when we developed the series that there was risk involved but unfortunately, once we saw the finished series, it became clear that the programme fell on the wrong side of that line."
Channel X's managing director, Alan Marke, said: "I am incredibly disappointed about this decision as I am very proud of this project and all the talent involved.
"But I understand the world has changed since the series was originally commissioned and sympathise with the difficult decision the BBC has had to make."
The Catholic Bishops' Conference of England and Wales welcomed the decision to withdraw the programme.
The Right Reverend Crispian Hollis, Bishop of Portsmouth and spokesman for the conference said: "I am delighted that this has been withdrawn.
"It was obviously going to be a controversial programme which would have caused offence, not least among the Catholic community who hold the person of the Holy Father in the highest regard and affection.
"Any attempt to belittle or diminish his status as the leader of the Catholic Church is totally unacceptable, and not only to Catholics," he added.