The 22-year-old, who is out of contract in the summer, has missed the whole season with a knee injury and he has now had to undergo another knee operation.
Flanagan, who made 23 appearances for Liverpool last season, suffered the original injury in pre-season and had been targeting a return but Press Association Sport understands a scan of the knee revealed another problem requiring surgery.
Flanagan was on the standby list for Roy Hodgson's England squad and Liverpool boss Brendan Rodgers said in March he hopes a new contract will be agreed with the defender.
Rodgers said then: "He is working his way back to fitness and when that happens I am sure the contract will get sorted out.
"He is a big part of the future here. He did remarkably well last year and showed he is player who can play for many years at this level."
