The actor had this to say on the subject:
"Everyone on Twitter tries to make it like it's my decision, but the bottom line is I was not asked."
"[The producers] don't want to put Jack in it. And I know fans are really upset about it, as was I."
"People have tried to say it's my schedule - it's absolutely not. I was told by the producers of Arrow that if I was asked to do the 50th anniversary of Doctor Who they'd let me go and do it."
"It was nothing to do with my schedule. It's just a matter of fact that I wasn't asked."
"I understand why they did it. They want to move forward, they want to try some different things."
"I know from how [former showrunner Russell T Davies] approaches things, they're not doing it just for the uber fan; they're doing it for the wider audience. And if they're going to bring a character back it wouldn't be just for the uber fan, it would be for everybody. So perhaps that's the thinking they had."Barrowman previously announced that he was in talks with the BBC for the special, before toning the nature of said talks down in a radio interview. He has more recently confirmed that he will not appear in the 50th Anniversary Special altogether.
Matt Smith, David Tennant, Jenna-Louise Coleman, Billie Piper, John Hurt, Jemma Redgrave and Joanna Page have all been confirmed for the special, which airs in November this year.
[Source: Digital Spy]