The Stephen Curran-owned eight-year-old, who finished second to Sir Des Champs in the Hennessy Gold Cup at Leopardstown on Saturday, was diagnosed with the problem on Monday.
He is instead likely to be aimed at the big Aintree meeting in April.
Casey said: “He’ll be out for two to three weeks.
“It’s a bad lung infection. The vets found he had it today.
“He’s going to be all right in the long term, but I would say Cheltenham is very unlikely now.
“The jockey (Andrew Lynch) thought something was wrong on Saturday and it looks like he was right.
“We’ll probably look at Aintree now.”
Flemenstar holds entries at Cheltenham in the Betfred Gold Cup, the Ryanair Chase and the sportingbet.com Queen Mother Champion Chase.
Michael Winters meanwhile will closely monitor weather conditions before deciding whether to run Rebel Fitz and Missunited in the Red Mills Trial Hurdle at Gowran Park on Saturday.
The County Cork trainer reports both horses in fine shape after their mid-season break but he will not risk them on testing conditions.
“The weather forecast doesn’t look too good. We had desperate rain on Sunday night so the ground might come very heavy,” said Winters.
“Both horses are in great order, they are fit and healthy, but I wouldn’t want to pulverise them.
“We’d love to get a run into them and there are other races to think about.
“There’s a race at Mallow (Cork) and the owners might want to go to Cheltenham.
“If the going’s bad we won’t run them but if they put Gowran off for a week we might have another look.
“Both horses are in great order and they are fit and healthy.”
Four of the 12 entries for this Grade Two contest over two miles are from the Willie Mullins stable – Midnight Game, So Young, Thousand Stars and Zaidpour.
The list is completed by Arnaud, Noble Prince, De Valira, Fosters Cross, Hisaabaat and Rory O’Moore.
Rubi Light meanwhile will attempt to win the Red Mills Chase for the third successive year.
Trainer Robbie Hennessy is looking forward to running the eight-year-old in the Grade Two contest over two and a half miles ahead of going for the Ryanair Chase at Cheltenham next month.
Rubi Light has finished third and fifth in the last two runnings of the Grade One Ryanair over two miles and five furlongs.
“I’ve taken him out of the Queen Mother at Cheltenham and he’ll go for the Ryanair again,” said the County Meath handler.
“First it’s the Red Mills Chase at Gowran. He’s won it the last two years. Hopefully the racing will go ahead on Saturday.
“He’s in great form. We gave him a bit of a break and he’s back now.
“He worked the other day on the Curragh – Andrew Lynch rode him – and we’re very happy with him.”