The actress tells Vulture she feels like "a political wife" when she is asked to comment on claims made by five women, suggesting the Oscar nominee acted inappropriately and abused his power.
"That annoys me," she says. "I have been asked to answer for him and I have nothing to do with it... I feel like a political wife or something. I don't like that."
Gyllenhaal recently admitted her opinion of Franco "changes all the time," and despite the claims, which he has called "inaccurate," "The Deuce" producers, including Maggie, decided not to ditch the actor from his central dual role as twin brothers Frankie and Vincent Martino in the 1970s porn industry drama.
"I feel like it's important to continue making the show," she adds.
Four of the women who have accused James of sexually exploitative behaviour were students at his Studio 4 acting school. He is alleged to have removed protective plastic vaginal guards during a sex scene, and of pressuring women to bare their breasts on set.