Hough has been partnered with Olympian Shawn Johnson for the show's current all-star edition.
UsMagazine.com said he aggravated a pre-existing neck injury during the program's Oct. 30 broadcast and couldn't dance on Monday night's show, so Ballas subbed for him.
"Derek's injury is really serious," a show insider told UsMagazine.com.
"It's likely Mark will finish out the season for him," the source said. "Derek is so disappointed but very badly hurt. He needs surgery."