Flintoff, speaking to the London Evening Standard at a Sky TV party on Tuesday, criticised Atherton's work as a Sky commentator and cricket correspondent for The Times newspaper.
"He's a prick," said Flintoff of fellow former England captain Atherton. "He's a f****** prick. He sits there making judgments about players that are much better than he ever was, believe me, he's a prick."
Flintoff added: "How can he talk about a player like Alastair Cook who is 10 times the player he ever was? He has a much bigger average and will go on and on. Atherton averaged in the 30s for England and yet he thinks he can judge others."
Asked if he wanted his comments taken as 'off the record', Flintoff replied: "I don't care. Say what you like. There's no love lost there."
When opening batsman Cook was made England's one-day captain last year Atherton, himself a former opener, described the left-hander as a "plodder" with the bat and a "donkey" in the field.
Tuesday saw Cook score his fifth hundred in 47 one-day internationals and third in six matches, after he'd effected a dynamic run-out in the field, as England beat the West Indies by eight wickets at The Oval to take an unassailable 2-0 lead in a three-match series
Atherton, who has modified his comments regarding Cook since his now infamous 'plodder and donkey' remark, by contrast managed just two hundreds in his 54 one-day internationals.
Cook, still only 27, also has a superior Test record with 19 hundreds in 80 matches at an average of nearly 49 compared to Atherton's 16 centuries in 115 Tests at nearly 38.
Atherton's relationship with Flintoff is said to have become strained when in 2006 he wrote: "The only positive benefit of the injury to Flintoff may be the end of his immediate captaincy ambitions."
Under Flintoff's captaincy, England suffered a 5-0 Ashes thrashing during their 2006/07 tour of Australia.