The Daily Star recently claimed that McIntosh's Silurian warrior, who appeared in 2011 episode 'A Good Man Goes To War', would become infatuated with Jenna-Louise Coleman's new companion during the sci-fi's upcoming seventh series.
A source allegedly said: "[Showrunner] Steven Moffat loves to shake up the show. What better way than a lesbian storyline?"
However, McIntosh has since taken to Twitter to dismiss the rumors, posting: "Just to say I have no idea WHAT the Star is talking about! No-one's asked me..."
After a fan enquired about the possibility of a return for Madame Vastra, she replied: "I wish... Still thinking up plot lines to pitch to mr Moffat."
When another user pointed out that many Doctor Who fans wouldn't believe her denial, she admitted: "I know cos even if it's true I can't say! But really we're talking about the daily star...."
"I think I might revisit them," Moffat said. "They were great fun to write... I was pleased by the reaction to them, but not surprised. They really cut through as characters, given how little screentime they had.
"I certainly wouldn't be averse to them returning. It's just a thing that worked, isn't it? I love that Victorian setting, and having kicked it out of Sherlock Holmes I can always kick it in somewhere else!"
Earlier this month, the Daily Star also reported that classic villains the Ice Warriors are due to feature in series seven.
Doctor Who will return to BBC One in the UK and BBC America in the US later this year.
> 'Doctor Who': Matt Smith and Jenna-Louise Coleman in new photo
> 'Doctor Who's Jenna-Louise Coleman companion name revealed?
Watch a trailer for series seven of Doctor Who below: