The Denmark international, 23, will undergo surgery on his troublesome foot injury early next week after being sidelined since September.
"It's a blow for Daniel but we want to get his problem sorted," Rafa Benitez told the club's official website.
"We have defensive cover and Martin Skrtel is playing very well, Daniel will be back for next season."
Agger has only played six games for Liverpool this season and his absence is a blow for the club who have key games coming up in both the Premier League and, most notably, the Champions League.
poor thing. hope he can get well soon!
sian..agger my fav player. Good defender, not bad shooter. He will be missed. Hope his surgery gets better.