The 31 year old striker missed the trip to Sheffield Wednesday with the illness and was withdrawn shortly after half time in the game against Norwich at the weekend.
Mackay has confirmed that Maloney was sick during the half time break against the Canaries and is a doubt for the weekend's game with Watford.
Speaking to the Wigan Evening Post Mackay said: “It’s taking Shaun time to fully get over this bug. We had him in Tuesday morning to see the doc, and it’s just a matter of time to let it run through his system.
“He seemed to be a lot better at the end of last week, and had no problems about starting the game against Norwich.
“But at half-time he wasn’t feeling well, and we have to be careful with him. It’s out of our control.”
Maloney has been linked with a move away from the club in January with Everton being linked with a move for hte striker who's contract expires in the summer.