The BAFTA-winning writer's detractors have accused him of misogyny in the past, specifically after an extract from an interview Moffat gave in 2004 surfaced online.
In the article, Moffat seemingly described women as "needy" and "hunting for husbands", although he later claimed the extract was from the viewpoint of a character on the TV show Coupling.
He's also been criticised in some quarters for apparently writing female characters who exist solely around the purpose of aiding the Doctor in the BBC One series.
However, Capaldi has defended the Sherlock writer, and can't see any truth to the critics' accusations.
"I think we've done great stuff," Capaldi told SFX Magazine.
"I think Steven's fabulous. I don't know why people have a go at him, why they call him a misogynist. I don't understand that at all. I think he's a brilliant writer."
During the interview, the actor also defended the quality of the long-running drama, following Moffat's recent comments that a lack of budget prevents the series being "as good as it should be".
"The fact of the matter is any show that's making 12 episodes a year, with these budgets and under these circumstances, not every [episode] is going to be fantastic," he added.
"And certainly not every [episode] is going to be to everyone's tastes. Fandom is so rich and diverse that you're absolutely guaranteed to be disliked by a whole pile of people somewhere.
"But I think [Steven] has done amazing stuff. To push the envelope of what Doctor Who can be, while hanging onto it, is hard, especially when it's so successful it becomes a victim of its own success, because as a kind of brand it's encouraged to do the same thing."
Until then, we have the new series to look forward to. Speaking of which...
Doctor Who returns April 15 on BBC One.
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