Assistant Graham Barrow will take temporary charge
Wigan say manager Warren Joyce is recovering from surgery after undergoing a "minor but important procedure" which "required immediate attention".
Assistant Graham Barrow, who has been placed in temporary charge, says it was "as serious as any health issue can be".
Joyce had the operation on Tuesday after having a routine medical examination on Monday.
It is expected he'll make a full recovery.
"It’s a much more serious situation being sat here with you this time because when it concerns somebody’s health it’s alarming. I’m not trying to say when somebody has been sacked it’s not serious, but this is much more personal to Warren and his family," Barrow said on the Wigan club website.
"I spoke to him this morning though and he’s kept in touch with us all from his operating bed almost which is just typical of him. He’s feeling a bit better but he’s not quite right yet to come into training. We did see him shortly yesterday and he didn’t suffer a setback as such, but he was feeling really tired afterwards."
In a statement, Wigan had confirmed that "Warren Joyce underwent surgery on Tuesday for a minor but important procedure which required immediate attention".
On the pitch, Wigan are second from bottom in the English Championship, two points from safety.
The Latics face fellow relegation threatened second tier club Blackburn Rovers on Saturday.