The 2009 tourist had an arthroscopic examination on his left shoulder this morning and is now expected to be out of action until December.
Flutey joined French side Brive from London Wasps earlier this summer but has been restricted to just one appearance for his new club.
"I can't go on the way I have been," said Flutey, who won a Lions Test cap in the historic 28-9 victory over the Springboks on July 4.
"I can't go out and play at 80%. I need to get it sorted."
The injury first became apparent in January but Flutey was bale to manage the problem and went on to feature in the Six Nations and then in six tour games for Ian McGeechan's Lions.
As well as missing Top 14 and Heineken Cup fixtures with Brive, Flutey will also be unavailable for England's November internationals against Australia, Argentina and New Zealand.