The writer told the New York Times that it would be "quite hard" for the show's central characters to collide.
"I think there are problems of doing that," he admitted. "Because then you would say that Sherlock Holmes lives in the same world as The Doctor, and there are Daleks and all sorts of things. If a Sherlock Holmes story depends on time travel being impossible, it's quite hard [to do it] if he's a personal friend of The Doctor's."
However, he admitted that fans of both shows have often enquired about the potential crossover.
"I think everyone who's passing me in the street is suggesting that at the moment," he revealed.
Moffat also confirmed that work has begun on the next three-part series of Sherlock.
Doctor Who returns to BBC One for a Christmas special on December 25. The second series of Sherlock is expected to air in autumn 2011.