There have been calls for Wigan to part company with the 26-year-old Welshman, but Lenagan insists that he will be staying with the Warriors.
"This is not drug-taking; it is in a super-charged, emotional environment behaving irresponsibly. That is no reason to sack a player," he told Sky Sports News.
"That is a reason to discipline him, a reason to make sure that he suffers from it - because we as a club have suffered as well, and quite rightly so, because we are responsible for our players - but there is no question of us sacking Ben Flower."
Flower joined Wigan from Welsh side Crusaders in 2011.