The board has told the pair to settle their differences but Flintoff, who was outstanding in England's Ashes series victory this summer, concedes that Ganguly, who has captained India in 49 Tests, can be an awkward character.
Flintoff, who played alongside Ganguly when he spent a season as Lancashire's overseas player in 2000, writes in his autobiography, Being Freddie: "Ganguly just didn't work out at all. You can accept a player not playing well, because we all have our ups and downs, but he just didn't want to get involved.
"He wasn't interested in the other players and it became a situation where it was 10 players and Ganguly in the team. He turned up as if he was royalty, it was like having Prince Charles on your side.
"He turned up for his first net session with Lancashire, when you would have thought he would have wanted to make a good impression, and got hit on the back of the knee. Those sort of blows do hurt, but you normally rub it a bit and make sure you grin because everybody else is laughing. Ganguly didn't see it that way and got the hump and we didn't see him again for two days."
Flintoff is due to face Ganguly again when England tour India in the new year. The all-rounder famously ripped his shirt off in celebration after winning a one-day match on the last tour there four years ago, an act Ganguly copied after India won the 2002 NatWest Series.
"We say hello to each other now, but it doesn't go any further than that. I don't dislike the bloke, but it's a struggle with him," Flintoff writes.