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Liverpool assistant manager Thompson has taken charge while Kop boss Gerard Houllier is convalescing after major heart surgery three months ago and the club have endured a disastrous slump.
And Case believes the £11million sale of Robbie Fowler to Leeds will come back to haunt Liverpool, especially as Michael Owen is struggling with an ankle injury.
Case, who moved from Anfield to Southampton, was working as a radio pundit at Liverpool's 2-0 defeat at St Mary's Stadium. He says the sooner Houllier returns the better.
"Phil is a good No 2 in terms of motivation and his heart is there for the club. But as a manager, I just feel that Houllier is the top man.
"I think Phil would have been asked to become manager a while ago if he was the material the club was looking for.
"It's difficult looking from the outside, but I'm not just picking at results. I know Phil and he has great enthusiasm for the game. On the hard-core decisions about things like formation I know they speak collectively, but the final decision would be down to Houllier and I'm sure they are missing him."
Thompson enjoyed a purple patch when he took over from Houllier in mid-October, but Liverpool's alarming slump has seen them blow the leadership.
They have gone from being 11 points clear of Manchester United with a game in hand to being a point behind Sir Alex Ferguson's title favourites, having played the same number of matches after their defeat at Southampton on Wednesday.
Liverpool have taken just six points from their last seven games and face title rivals Arsenal at Highbury on Sunday, quickly followed by games against United and Leeds.
Their biggest problem is a lack of goals. Owen is injured, Jari Litmanen is not a natural goalscorer, Emile Heskey has managed just one since September and loan signing Nicolas Anelka has yet to rediscover his sharpness.
The biggest irony is that they sold their most natural goalscorer in Fowler to Leeds, who are now reaping the benefits as three straight wins have taken them back to the top of the table.
Fowler could not handle Liverpool's squad rotation and Case insists that system is another reason behind their faltering challenge.
He said: "All footballers want to be playing and when you're on form you can't wait for the next game. But if you're left sitting there watching the game it's very disheartening.
"Robbie was a prime example. His goalscoring touch and linking up with his teammates takes time to build up.
"Robbie is now showing the whole country what he does best and if he can do it at Leeds then he could surely have done it at Liverpool.
"He is still scoring goals and doing what he's very good at, given a proper run. Something must have gone on because, personally, I would have Robbie in there ahead of Anelka.
"They want Anelka to take the pressure off Michael Owen but they are still trying to find a formula that will fit Anelka."
He added: "Consistency is the key and, whether you're playing badly or great, you still have to win your games. United have proved that by winning six on the bounce and suddenly they are right back in there."
There is still no indication of when Houllier will return but Case believes he will not be able to stay away. Case said: "I'm sure he will definitely come back, very much in the way Graeme Souness did. It's in the blood."