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 rumours, 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...."
Moffat previously told SFX that he was keen to revisit the characters of Madame Vastra and her maidservant Jenny (Catrin Stewart).
"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!"