The BBC told Digital Spy that the actor, who played the Ninth Doctor in the show, was never fully attached to the special and that his decision to not take part in it has had no impact on the special's production.
An official source had this to say about Eccleston's decision:
"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."
Two Doctors, Matt Smith and David Tennant, are already confirmed for the special, set to air in November this year.
[Source: Digital Spy]