The Irishman has accused Benitez of focusing on Europe - so to look good for interested clubs on the continent.
Whelan, 48, who won 12 major trophies in a glory-filled career, said: "It's all gone wrong with the manager and he's shown exactly where his priorities lie.
"He wants to win the European Cup so he can get a job in Europe. For me, his days have got to be numbered at Liverpool.
Whelan, speaking on Ireland's RTE Television, added: "He's taken players off who are the only players who are going to give you a chance of winning the game.
"And he drags them all off because he's got a game on Wednesday.
"When I saw the team I thought he's not bothered about this game. He's putting all his eggs in one basket and I can't see why he's done it."