Lewis aired his views regarding the current situation at the Ravens as a pundit for ESPN on Monday Night Football this week.
The former linebacker - who spent 17 years with the team before retiring in February - said: "When you think about the Baltimore Ravens and the transition that they went through, they're missing leadership right now.
"They're going to have to refocus and find some leaders in that locker room very quickly."
However, Flacco has hit back his former teammates comments, telling The Baltimore Sun: "It is what it is. Ray knows better than that. Things happen.
"I think we're usually a pretty good team with stuff like that. If you look around the league, there are probably a lot of leadership problems then. Like I said, Ray knows better."
Lewis made the comments following an incident on Sunday night in which Ravens wide receiver Jacoby Jones was struck in the head by a stripper with a champagne bottle at a birthday party.