Whelan claimed the Reds were in a "mess" following Wigan's 1-0 victory over Benitez's side on Monday.
Whelan said: "Liverpool are in a mess. The owners, being American, I don't think they feel what we [fans] feel."
Reds manager Benitez hit back: "I do not talk about Wigan. He [Whelan] should talk about his own club."
Whelan also admitted he felt sorry for Liverpool fans after Hugo Rodallega's volley consigned them to a seventh league defeat away from Anfield this season, and their ninth loss in total.
"The big sympathy I have is for the Liverpool supporters because they are a fantastic lot," Whelan added.
"I'm really, really sorry for their supporters. We went to Anfield earlier in the season and there was absolutely no atmosphere and no heart at all.
"The supporters feel that and I think the players are starting to feel it."
Monday's result left Liverpool in sixth place in the Premier League table, one point behind Tottenham and Manchester City who have one and two games in hand respectively over the Reds.
Aston Villa, who are three points behind Liverpool, have three games in hand as the race for fourth spot, and a place in next season's European Champions League, gathers pace.
Benitez was highly critical of his side's performance at the DW Stadium, accusing them of lacking attitude and character.
But the Spaniard has little time to dwell on the defeat with the Reds travelling to France to take on Lille in the Europa League on Thursday.
"Hopefully there will be a reaction in Lille," said Benitez. "This is an opportunity to put things right and try to get a good result.
"In football you sometimes prefer to rest but at this time it is good to have a match quickly after what happened at Wigan."
Source: BBC Sport