The Scotland international will undergo surgery to repair a long-standing problem that the 30-year-old is thought to have aggravated while on international duty in September.
"When my team and I this summer Shaun had already suffered from an existing hip injury, but had chosen to play through those problems as we all thought they would be manageable over the course of the season," Coyle told the club's official website.
"However, when he was on international duty with Scotland he picked up a back injury which stemmed from the previous hip problem and when he returned it was clear he wasn't himself on the pitch.
"I can't give an exact timescale on how long he'll be out for until the surgeon takes a proper look at it, but it certainly will be several months.
"It's a blow to lose such a top player, but we still have tremendous quality in our ranks and players who are motivated towards doing well for Wigan Athletic."
Maloney's last appearance for the Latics came in a 2-0 defeat to Leicester in September.