The former England all-rounder ended his career in 2009 after struggling to recover from a knee injury, but announced that he would join Lancashire Lightning for the Twenty20 tournament earlier this week.
In his column in The Mirror, Botham said: "While I wish him all the very best, I think he is making a massive mistake. We've not seen Fred on a cricket field since those memorable days in 2009, and five years is a long time out of the game.
"For those that can't remember that far back, Fred had no choice but to quit cricket because of a chronic knee injury that had made walking difficult let alone bowling at 90 miles an hour.
"To come back after five years out of the game and with that injury still in the background is a huge risk. I just hope he does not let himself down too badly."
Flintoff is expected to make his first appearance for the team when they face Yorkshire Vikings next week.