The actress, who has appeared as Gwen Cooper in both shows, told The Independent that any further crossover seems unlikely.
She explained: "We have lots of adult themes running in Torchwood and I think it would be inappropriate for us to have anything to do with Doctor Who because it's predominantly a family programme."
Myles added that spinoff series Torchwood "deals with darker subjects" than its parent show.
"If they want to do [a crossover], then fine but I can tell you that I'm not involved in it," she said. "They won't give me guns or a bazooka!"
Doctor Who showrunner Steven Moffat previously hinted that he has "various plans" for the show's 50th anniversary on November 23, 2013.
"All I can say emphatically is it will be huge," he teased. "There's lot of decisions we're making that are about making all that possible. It'll be amazing."
Doctor Who will return to BBC One this Christmas for a festive special. A short preview of the episode will air as a part of this year's Children in Need broadcast.
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Watch Eve Myles discuss the last series of Torchwood below: