Moffat addressed the scheduling concerns via Twitter this week, Zap2it.com reported.
"Misquotes and misunderstandings," Moffat said in his online posting. "But I'm not being bounced into announcing the cool stuff before we're ready. Hush, and patience."
The Guardian newspaper referenced another tweet from Moffat, which said Thursday: "The scheduling of Dr Who has got NOTHING to with Sherlock. On the plus side THE BBC SPELLED MY NAME RIGHT!!!!"
A BBC network executive had said the next season of the long-running show won't have the normal 13 episodes because Moffat is still working on "Sherlock."
"[Moffat] needs enough time to get that done and then start work on the next series of 'Doctor Who,'" BBC One controller Danny Cohen said at this week's Church and Media Conference in Derbyshire. "So there will be ['Doctor Who'] episodes, but not as many.
"There's only so many hours a day [Moffat] can be awake. The man has to sleep and eat, and he's got a family. ..."
The British broadcaster recently announced it had renewed the mystery series "Sherlock" for a second season.
It also confirmed last week it had ordered a fresh run of episodes of the long-running science-fiction show "Doctor Who," although it did not say whether all of the installments would air in 2012.