Botham insists that Flintoff should take a break from the game towards the end of the year, instead of going to India, to prepare for the World Cup in the Caribbean in 2007.
He also believes the player should join him on his next cancer charity walk.
Flintoff already has a busy 2006 ahead of him with home Test matches against Sri Lanka and Pakistan and then the defence of the Ashes in the winter.
"I don't know what the ICC Champions Trophy is all about. Slotting it in five months before the World Cup is beyond me," Botham said on Thursday.
"I think it's greed taking over from common sense. They are killing the goose that lays the golden egg.
"It wouldn't surprise me to see a lot of second teams playing in the ICC Trophy. I think there must be a strong case for England players, if they have had a hard summer, to miss it."
Flintoff has already promised to support Botham on his 11th charity walk which begins in Belfast on October 9 and will see him flying by helicopter to take in two cities a day before finishing his hectic schedule in London on October 17.
Botham has already trekked 6,500 miles and raised more than eight million pounds for cancer charities.
"Freddie has promised his support and will be doing more than one town. The other England boys are coming along at various stages," said Botham.
Botham maintained he was serious when he suggested it would do Flintoff more good to take a break and join him on the walk rather than risking burnout by adding to his already daunting cricket schedule.
"If I was Andrew Flintoff I would say I'm looking forward to the summer and I'm looking forward to Australia and in between I'm on holiday," he said.
"Forget the ICC Trophy. Freddie has learned a lot and is more streetwise now. He knows what he has to do and what his body can do. Andrew Flintoff has to do what is best for Andrew Flintoff, in my opinion."
Botham is certainly not underestimating the challenge facing England this summer.
"The Test matches are going to be extremely tough, this summer is a massive challenge," he said.
"They have got to steamroller Sri Lanka and they've got to beat Pakistan."
Then, he believes, England can go to Australia and successfully defend the Ashes they won in last summer's epic Test series which put English cricket firmly back on the world map.