While he praised McGann's "superlative" performance in recent online special 'The Night of the Doctor', Moffat suggested that it could prove confusing to have more than one actor play the Doctor on a long-term basis.
"This [50th anniversary] is a party time, so we're doing things differently," the BBC drama's head writer told the press at the official Doctor Who Celebration at London's ExCel.
"One Doctor at a time is the real rule - 'Who would be on the lunchbox?' is always my question when we talk about having more than one Doctor."
Moffat added that Doctor Who will now return "militantly" to the idea of featuring just one Doctor at a time.
"I have a slight paranoia that at the moment it seems like every bugger's playing the Doctor - more or less all of Equity!" he joked. "Quite soon, it's going to go back to… 'There is one Doctor and that's who he is' - he's one man with many faces, he's not a committee of people with unusual hair."
Doctor Who's 50th special 'The Day of the Doctor' attracted an overnight audience of 10.2m viewers on Saturday (November 23), with those figures later being adjusted to 11.8m.
The series will return to BBC One this Christmas.
> Paul McGann: 'I would do more Doctor Who' - video
Watch 'The Night of the Doctor' in full below: