David Dunn and Chris Samba both missed Saturday's 5-0 thrashing at Chelsea due to illness and a handful of team-mates have now been laid low.
Reports have claimed that the virus which has hit the Rovers squad could lead to Allardyce requesting a postponement of Tuesday's clash with Peterborough.
Allardyce confirmed a virus has struck his squad and hopes his players will all have recovered in time for Saturday's game against Premier League champions Manchester United.
"Dunny and Chris Samba have a virus and a couple of the other lads who were playing against Chelsea have that virus or we think they are coming down with it," Allardyce told the club's official website.
"We will hopefully get them back next week when we have to go to Old Trafford
"But it is one of those viruses that can see you out for up to six days so we'll have to see."
A Blackburn spokesman said: "A couple of cases of swine flu have been confirmed and other members of the squad and staff have complained of virus-like symptoms."
And the Premier League club also confirmed the cup visit of Peterborough will take place as planned.
Cub secretary Andrew Pincher said: "There has been speculation in the national media following confirmation of sickness within the camp, but we can reassure all supporters that the tie will go ahead as planned."
Allardyce also confirmed that Australian midfielder Vince Grella is close to returning to action after a thigh injury.
He added: "We'll take a look at him. If he isn't ready for Tuesday night then hopefully he'll be ready for Saturday."