Moffat, who worked on the sci-fi show from 2010 until 2017, claimed that he did not have any insider information on Piper's role, but feels that producers have hedged their bets.
The actor, who played companion Rose Tyler, appeared to replace Gatwa as the show's lead when the Doctor underwent a regeneration. Piper' described her return as a last-minute decision.
"This is such a minefield. I have to really engage with how I answer this," Piper told an audience about the appearance at Florida Supercon, according to Deadline.
"All I can say is, I was approached very last minute, and I can't talk about in what capacity, but I found it very emotional to film, and I think it's a really great ending."
Rose Tyler was the companion for both Christopher Eccleston and David Tennant's tenures as The Doctor. She appeared regularly on the show between 2005 and 2006 and was a supporting character during the 2008 season and also made a cameo in the 2010 New Year's special.
It is yet to be confirmed whether Piper will actually be playing the 16th Doctor or if the show's producers have another trick up their sleeve.
Moffat, though, did offer some advice for the qualities the next person in the role should strive for.
"Attractive, but odd," he said. "There's something utterly odd, a sort of benevolent, kindly, slightly incompetent impersonation of a human being. The Doctor is never quite right."
Moffat explained that the Doctor should be "off-kilter", but someone that "little kids would want to run up and take that [person's] hand and feel absolutely safe".
Moffat's comments arrive weeks after the BBC said Doctor Who "is going nowhere" despite concern among the fandom.
The BBC's new chief content officer, Kate Phillips, promised to keep the British family favourite on screens.
"Rest assured, Doctor Who is going nowhere," Phillips said at the Edinburgh TV Festival in August, with Lindsay Salt, the BBC's director of drama, saying the corporation was "committed" to bringing the show back.