The Spaniard is believed to be frustrated at chief executive Rick Parry's role in valuing potential new signings, limiting how much Benitez can spend on certain targets.
That structure in the Anfield boardroom is blamed for costing them the signing of Gareth Barry, the Aston Villa midfielder, in the summer, while Benitez has also missed out on Portuguese winger Simao and the then Sevilla full back Dani Alves because of Parry dragging his heels.
With more than 20 drafts of an extension offered and rejected, Benitez's future remains in limbo, with his former club Real Madrid thought likely to target him as their new manager in the summer.
But Alonso is confident the man who brought him to the Premier League will stay, despite his power struggle with the club's owners.
The Spanish international also played down fears of a mass exodus of Benitez's signings should the manager leave.
He said: 'They are in a tug of war, but these are questions between Benitez and the owners and they will be resolved for the best. It doesn't affect the team at all, but my personal bet is that Rafa will stay at Liverpool.
'I remember when he came here, they said that most of Valencia would follow him - Roberto Ayala, David Albelda, Pablo Aimar. None of them did. It was the same when Mourinho left Chelsea. Like me, most of the others have three year contracts. Are they worthless?'
In an interview published in Spanish newspaper As before the defeat to Everton in the FA Cup, Alonso also insisted that he intends to see out the remainder of his own contract at Anfield.
Alonso was thought to be on his way out of Anfield in the summer but a £16 million move to Juventus never materialised. Since then, the Spanish international has been one of Liverpool's best performers.
He said: 'Liverpool have everything a player could want, the stadium, the stories. We are improving and thanks to Rafa we are where we should be, competing for every trophy we enter.
'The way the fans here talk about former players is so emotional. I will be here for three years, I can assure you.'
Though Liverpool remain just two points behind Manchester United, their form since the New Year has been unconvincing and, after being knocked out of the Cup by Everton, they have now lost Steven Gerrard to injury for the next three weeks.
Gerrard will also miss England's friendly match against Spain on Wednesday.
The midfielder's absence will be a huge concern for Liverpool as they make the awkward trip to Fratton Park to play Portsmouth on Saturday.
Benitez said: 'He is an important player for us. It is always more difficult to play without him.
'But you can't change things so it is better to concentrate on the next game.'
With and Without Gerrard 2006/07-2008/09 With Gerrard Without Gerrard Games 92 8 Wins 52 3 Draws 27 3 Losses 13 2 Win percentage 56.5pc 37.5pc Points per game 1.99 1.5 Goals For 150 13 Average Goals For 1.63 1.63 Goals Against 65 5 Avg Goals Against 0.71 0.63