The pair both missed the 5-0 thrashing at Chelsea on Saturday, with Rovers concerned that other members of their staff could be affected.
Manager Sam Allardyce told the club's official website: "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.
"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 Rovers spokesman added: "A couple of cases of swine flu have been confirmed and other members of the squad and staff have complained of virus-like symptoms."