The Daily Star claimed that Eccleston - who played the Ninth Doctor in 2005 - had agreed to star in the special but pulled out as filming was about to start.
However, the BBC has now told Digital Spy that Eccleston was never attached to the 50th and that his decision has had no impact on production.
"Chris met with Steven Moffat a couple of times to talk about Steven's plans for the Doctor Who 50th anniversary episode," an official source said.
"After careful thought, Chris decided not to be in the episode. He wishes the team all the best."
The anniversary special - to be shot in 3D - will star Matt Smith (the Eleventh Doctor) and David Tennant (the Tenth Doctor) opposite Jenna-Louise Coleman (Clara) and Billie Piper (Rose).
Confirmed guest stars include John Hurt (Alien) and Joanna Page (Gavin & Stacey), while classic Who monsters the Zygons have also been confirmed to return.
> Matt Smith on Doctor Who 50th: 'It celebrates old Doctors'
Watch the stars of Doctor Who talk the 50th special with Digital Spy below: