Blackburn assistant manager Neil McDonald has confirmed Sam Allardyce kept away from his players during the win over Peterborough United on Tuesday.
Rovers claimed a 5-2 victory over the Championship side to book their place in the quarter-finals of the Carling Cup.
Blackburn are recovering from a bout of swine flu which has affected the club, and Allardyce spent the whole of Tuesday's match in the stands rather than on the touchline because he was feeling unwell.
"He is feeling a little unwell, so he sat upstairs as he wanted to see the picture from above,'' McDonald told Sky Sports. "He trusts in his staff which is excellent, and he was at the game but he didn't want to take any chances. He shot out just to make sure nobody gets what he might have.''
McDonald said there were no new cases to report of players having fallen sick.
"It's under control. We had a squad up on Monday and everyone came through from that squad which was great,'' McDonald said. "We will monitor it on a 24-hour basis. Everyone seems okay.''
The Health Protection Agency has warned players that spitting on the pitch could increase the risk of passing on infection during matches and McDonald said that the club was doing everything in its power to ensure the virus did not spread.
"I'm not a medic so I don't know how it is passed on, but you can spit, cough, sneeze - anything that comes out of your body is how it is passed on I suppose,'' he said. "I think there is always a problem in it spreading, but we are doing our best to try and contain everything by doing the right things and monitoring everyone, and we will continue to do that. Hopefully it won't spread any more, fingers crossed.''
A spokesman for Blackburn confirmed that Allardyce was not at the club's training ground on Wednesday morning but would be back at work on Thursday.
The spokesman said: "He (Allardyce) said he would just be off today - but everybody is off today and will be back in tomorrow. Every time after a game, especially after a night match, they have the day off. Only the players that were not involved in the game will be in today.''