The Sherlock writer argued that the Time Lord - currently played by Matt Smith - would not be an appropriate addition to the more adult spinoff series, but teased that John Barrowman's Captain Jack Harkness could continue to appear in both programmes.
"The Doctor could never go to Torchwood," Moffat told TVLine. "[Torchwood executive] Russell [T Davies] and I both agree on that. Doctor Who has a tremendous relationship with children in Britain. They'd want to watch Torchwood then, and it's not really a children's show."
Moffat further teased that he had planned for Captain Jack to cameo in Doctor Who's most recent episode, 'A Good Man Goes To War'.
"I'd have [brought back Captain Jack] for 'A Good Man Goes To War', but John was busy doing Miracle Day... When we've got a good story, we'll do it. You can't just bring somebody back and say, 'That's a story'.
"I won't be thinking, 'How do you bring Captain Jack back?' I'll be thinking, 'You know what this needs? We need to bring Jack back for it'."
Barrowman previously declared that he would return to Doctor Who "at the drop of a hat". He revealed at Comic-Con last week that he would love a role on Doctor Who's 50th anniversary in 2013.
> Doctor Who return date confirmed, "huge" twists teased at Comic-Con
> John Barrowman talks Torchwood: Miracle Day: 'We delve into Jack's past'
Watch John Barrowman discussing Torchwood: Miracle Day with Digital Spy below: