Rovers were without Chris Samba and David Dunn for the 5-0 defeat to Chelsea at Stamford Bridge on Saturday due to what manager Sam Allardyce has described as a virus.
It has not been confirmed if they are the two who have been diagnosed with swine flu.
Blackburn would have needed to apply for special dispensation from the Football League to postpone the tie against Peterborough, however they are happy to play the match.
Rovers club 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 the tie will go ahead as planned."
Earlier, a Blackburn spokesman had stated: "A couple of cases of swine flu have been confirmed and other members of the squad and staff have complained of virus-like symptoms."