Eccleston has been largely tight-lipped about his time on Doctor Who since departing in 2005, but did reveal last year that he quit the show over "politics".
In a new interview with The Telegraph, the actor contended that he acted honourably in bowing out of the role after his brief tenure as the Ninth Doctor.
"I know what went on and the people who were involved know what went on - that's good enough for me," Eccleston said, adding: "My conscience is completely clear."
The actor continued: "I've lived my life, particularly my working life, on the basis that I have to be able to look at myself in the mirror about the way I behave. It wasn't a bold move, it was an entirely natural one.
"I'm hugely grateful to the children who to this day come up and talk to me about the show."
Eccleston has previously denied that he would return for Doctor Who's 50th anniversary in 2013 because he doesn't like revisiting his past work.
"I never bathe in the same river twice," he told Graham Norton last May.
Matt Smith's current incarnation of Doctor Who returns for its seventh series this autumn.
Karen Gillan and Arthur Darvill will be leaving mid-series, to be replaced by Jenna-Louise Coleman as The Doctor's new companion.
