The BBC also admitted that in a statement issued last week it falsely attributed comments to Eccleston, in which he "hoped viewers continued to enjoy the series".
Jane Tranter, BBC controller of drama commissioning, said: "The BBC regrets not speaking to Christopher before it responded to the press questions on Wednesday March 30. The BBC further regrets that it falsely attributed a statement to Christopher and apologises to him."
Rather than the shock exit, as Eccleston's departure has been portrayed, Tranter admitted the the BBC had known he was going for months.
She said that the BBC knew as far back as January that Eccleston intended to quit and made an agreement that any announcement would be "done jointly". She also backtracked on press statements that Eccleston was quitting for fear of being typecast or because of the gruelling schedule.
David Tennant, who is starring in BBC drama 'Casanova', which along with 'Doctor Who' is written by Russell T Davis, is the bookmakers' favourite to take over the role for the already commissioned second series.
Tennant also starred in the first live drama broadcast by the BBC in 20 years last Saturday, a remake of 1950s science-fiction cult hit, 'The Quatermass Experiment'.
So far, 'Doctor Who' has had a successful return to television after a 16-year absence. The first episode, broadcast on March 26, pulled in an average of 9.9m viewers. Although losing 2.6m viewers for the second episode last Saturday, it still beat main rival in the slot, ITV's 'Ant and Dec's Saturday Night Takeaway.'
Up for a part in the new series is 'Space' and 'Shaun of the Dead' actor/comedian Simon Pegg. He is to star in episode seven of the current series, in which will play an evil character called The Editor, who is in charge of the 500th floor of a building from which time travellers can not return from.
"I'm in one episode of the new 'Doctor Who'. I think it's going to be spectacular. It's a real honour to be in it. To be a 'Doctor Who' villain was a bit of a dream come true, so I was very happy to do that," Pegg said.
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