The 28-year-old actor, who has previously defended Gillan's short skirts and kissogram outfit, shrugged off claims that the sci-fi drama had crossed the line.
"Don't tell me that the dads at home don't go, 'Ah cool, Karen's on'," The Sun quotes Smith as saying. "What do people want Karen to dress in? A floor-length skirt, a pair of jeans and a hoodie? She's a beautiful woman."
Following Smith and Gillan's first appearance in 'The Eleventh Hour' last April, the BBC received a number of complaints from viewers.
Smith continued: "Amy Pond is a sexy character by her very nature. No one is quite like Amy. I think Doctor Who should be dark. I think it should be scary."
Referring to the Third and Fourth Doctor's assistants, he added: "And sexy? I mean, for God's sake, look at the companions of Jon Pertwee and Tom Baker in their tiny, Tarzanian tops."
Smith concluded: "It will always be family entertainment and it has to adhere to that. But I don't think it has gone too far. I mean, how sexy is it?"
> Karen Gillan: 'Doctor Who' is not sexy'
> Matt Smith: 'Amy Pond is sexiest companion'
Watch the new Doctor Who trailer for episodes 8-13 of season six below: