Reports on Monday morning have suggested the Lancashire club may seek special dispensation from the Football League to postpone the tie against Peterborough, although no-one was immediately available at the club to confirm whether this was the case.
"Dunny and Chris Samba have a virus," Allardyce told the club's website.
"And a couple of the other lads who were playing against Chelsea have that virus or we think they are coming down with it.
"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."
Midfielder Vince Grella has also been missing since suffering a thigh injury away with Australia on international duty, but Allardyce is hopeful he will be back for Tuesday's match if it goes ahead.
Blackburn 1/2, Draw 3/1, Peterborough 6/1