The statement follows reports in the tabloid press that the actor had pulled out of the story just as filming was due to begin. However, the BBC makes clear the actor was never contracted for the story, which is currently in production.
A BBC spokesman explained:
Chris met with Steven Moffat a couple of times to talk about Steven's plans for the Doctor Who 50th anniversary episode. After careful thought, Chris decided not to be in the episode. He wishes the team all the best.
Eccleston played the Ninth Doctor when the series returned in 2005, staying with the show for just one season. In 2011 he gave an interview saying he left the series because of politics and because he did not see eye-to-eye with senior members of the production team. He has stated how much he enjoyed the role and fans had hoped he could be persuaded to make an appearance in the 50th anniversary special.
An appearance from the Ninth Doctor in the story may still be possible using archive footage from the series.
Filming has continued this week, with Gelligaer Common north of Caerphilly playing host to the TARDIS (times two) yesterday. Jenna-Louise Coleman was present for recording scenes involving her on the Doctor's anti-grav bike, and a helicopter was also present during the morning. You can read a summary of events up in the hills via the She-Goat: blog.
Meanwhile, John Hurt was at the BAFTAs yesterday, with the BBC report saying: "Hurt revealed he had come to the event from filming Doctor Who, for its 50th anniversary, in Cardiff."