The Discworld author previously said that the series is "ludicrous" and "breaks most of the laws of narrative".
However Gaiman, whose script for the show will air in 2011, told the BBC: "Doctor Who has never pretended to be hard science fiction.
"At best Doctor Who is a fairytale, with fairytale logic, about this wonderful man in this big blue box who at the beginning of every story lands somewhere where there is a problem."
Gaiman, who previously wrote Stardust and Coraline, also admitted that he felt powerful when writing the episode.
"I don't know what it's like to be God - obviously," he said. "Until that very first moment when you get to sit down and type the words in your script: INTERIOR. TARDIS.
"Suddenly I got a very good idea of what it must feel like. I went: 'I'm writing it now, this scene in the Tardis. I'm writing it!' And that was amazing. It was wonderful."